Ok, new information. It seems spindle operation is being disabled due to 
complaints about "unexpected real time delay", without any visible notation in 
LinuxCNC that anything has been disabled due to an error (poor form).

To summarize the setup:

The PC is one I built a year and a half ago, though I put in a new SSD dirve 
for this retasking of the PC. The PC is 100% dedicated to the lathe.

It's based on an ASUS F1A55-M LX Plus R2 motherboard, with an AMD A8-3850 CPU 
(4 core, 2.9 GHz) and 4GB of ram. I put a basic cheap video card in it since 
I'd read that the onboard graphics were often a problem, but this "unexpected 
realtime delay" seems to exist with either graphics adapter.

The install was from a USB thumb drive with the latest hybrid ISO image, 
installing LinuxCNC 2.6.3 with all it's defaults. I didn't have the PC on the 
'net when I did the install as I had to make a long cable to connect it, but I 
did do the available updates and upgrades later and they had no effect on this 
issue.

Output in syslog:

Sep 18 09:36:10 WPNet-Harrison kernel: [13163.505082] I-pipe: head domain RTAI 
registered.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.505090] RTAI[hal]: compiled with 
gcc version 4.7.2
(Debian 4.7.2-5) .
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.505207] RTAI[hal]: mounted 
(IPIPE-NOTHREADS, IMMEDIATE
(INTERNAL IRQs DISPATCHED), ISOL_CPUS_MASK: 0).
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.505210] SYSINFO: CPUs 4, LINUX 
APIC IRQ 2312, TIM_FREQ
12467830, CLK_FREQ 2892723000, CPU_FREQ 2892723000
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.505213] RTAI_APIC_TIMER_IPI: RTAI 
DEFINED 2314, VECTOR
2314; LINUX_APIC_TIMER_IPI: RTAI DEFINED 2312, VECTOR 2312
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.505216] TIMER NAME: lapic; 
VARIOUSLY FOUND APIC FREQs:
12467830, 12467830, 8495250
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.510950] RTAI[malloc]: global heap 
size = 2097152
bytes, <BSD>.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.511010] , <uses LINUX SYSCALLs>, 
kstacks pool size =
524288 bytes.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.511014] RTAI[sched]: hard timer 
type/freq =
APIC/12467830(Hz); default timing: oneshot; linear timed lists.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.511017] RTAI[sched]: Linux timer 
freq = 250 (Hz),
TimeBase freq = 2892723000 hz.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.511019] RTAI[sched]: timer setup 
= 999 ns, resched
latency = 2943 ns.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.519507] RTAI[math]: loaded.
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.572646] hm2: loading Mesa 
HostMot2 driver version
0.15
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.574214] hm2_pci: loading Mesa 
AnyIO HostMot2 driver
version 0.7
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.574252] hm2_pci: discovered 5i25 
at 0000:02:05.0
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.574535] hm2/hm2_5i25.0: Smart 
Serial Firmware Version
43
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.578984] Board hm2_5i25.0.7i76.0.0 
Hardware Mode 0 =
standard
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.581109] Board hm2_5i25.0.7i76.0.0 
Software Mode 0 =
io_spin
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.583752] Board hm2_5i25.0.7i76.0.0 
Software Mode 1 =
io_ana_spin
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.587239] Board hm2_5i25.0.7i76.0.0 
Software Mode 2 =
io_enc_ana_spin_fv
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713068] hm2/hm2_5i25.0: 34 I/O 
Pins used:
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713072] hm2/hm2_5i25.0:     IO 
Pin 000 (P3-01):
StepGen #0, pin Direction (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713074] hm2/hm2_5i25.0:     IO 
Pin 001 (P3-14):
StepGen #0, pin Step (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713076] hm2/hm2_5i25.0:     IO 
Pin 002 (P3-02):
StepGen #1, pin Direction (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713078] hm2/hm2_5i25.0:     IO 
Pin 003 (P3-15):
StepGen #1, pin Step (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713080] hm2/hm2_5i25.0:     IO 
Pin 004 (P3-03):
StepGen #2, pin Direction (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713082] hm2/hm2_5i25.0:     IO 
Pin 005 (P3-16):
StepGen #2, pin Step (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713085] hm2/hm2_5i25.0:     IO 
Pin 006 (P3-04):
StepGen #3, pin Direction (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713087] hm2/hm2_5i25.0:     IO 
Pin 007 (P3-17):
StepGen #3, pin Step (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713089] hm2/hm2_5i25.0:     IO 
Pin 008 (P3-05):
StepGen #4, pin Direction (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713091] hm2/hm2_5i25.0:     IO 
Pin 009 (P3-06):
StepGen #4, pin Step (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713094] hm2/hm2_5i25.0:     IO 
Pin 010 (P3-07): Smart
Serial Interface #0, pin TxData0 (Output)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713096] hm2/hm2_5i25.0:     IO 
Pin 011 (P3-08): Smart
Serial Interface #0, pin RxData0 (Input)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713098] hm2/hm2_5i25.0:     IO 
Pin 012 (P3-09):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713100] hm2/hm2_5i25.0:     IO 
Pin 013 (P3-10):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713102] hm2/hm2_5i25.0:     IO 
Pin 014 (P3-11):
Encoder #0, pin Index (Input)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713104] hm2/hm2_5i25.0:     IO 
Pin 015 (P3-12):
Encoder #0, pin B (Input)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713106] hm2/hm2_5i25.0:     IO 
Pin 016 (P3-13):
Encoder #0, pin A (Input)
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713108] hm2/hm2_5i25.0:     IO 
Pin 017 (P2-01):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713110] hm2/hm2_5i25.0:     IO 
Pin 018 (P2-14):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713112] hm2/hm2_5i25.0:     IO 
Pin 019 (P2-02):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713114] hm2/hm2_5i25.0:     IO 
Pin 020 (P2-15):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713115] hm2/hm2_5i25.0:     IO 
Pin 021 (P2-03):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713117] hm2/hm2_5i25.0:     IO 
Pin 022 (P2-16):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713119] hm2/hm2_5i25.0:     IO 
Pin 023 (P2-04):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713121] hm2/hm2_5i25.0:     IO 
Pin 024 (P2-17):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713123] hm2/hm2_5i25.0:     IO 
Pin 025 (P2-05):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713124] hm2/hm2_5i25.0:     IO 
Pin 026 (P2-06):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713126] hm2/hm2_5i25.0:     IO 
Pin 027 (P2-07):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713128] hm2/hm2_5i25.0:     IO 
Pin 028 (P2-08):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713130] hm2/hm2_5i25.0:     IO 
Pin 029 (P2-09):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713132] hm2/hm2_5i25.0:     IO 
Pin 030 (P2-10):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713133] hm2/hm2_5i25.0:     IO 
Pin 031 (P2-11):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713135] hm2/hm2_5i25.0:     IO 
Pin 032 (P2-12):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713137] hm2/hm2_5i25.0:     IO 
Pin 033 (P2-13):
IOPort
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713184] hm2/hm2_5i25.0: registered
Sep 18 09:36:10 WPNet-Harrison kernel: [13163.713186] hm2_5i25.0: initialized 
AnyIO board at
0000:02:05.0
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053265]
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053270] In recent history there 
were
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053273] 2891844, 2891612, 
2891869, 2891870, and
2892248
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053275] elapsed clocks between 
calls to the motion
controller.
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053285] This time, there were 
3728515 which is so
anomalously
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053288] large that it probably 
signifies a problem
with your
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053291] realtime configuration.  
For the rest of this
run of
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053294] EMC, this message will be 
suppressed.
Sep 18 09:36:11 WPNet-Harrison kernel: [13164.053296]

I have no idea where to go from here as this is getting into Linux/LinuxCNC 
internals.

Thanks,

   Pete C.


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