Please close this as invalid.  I discovered that by adding
"position_fix=1" to my alsa module options the capture problems go away.
For other people's benefit, here is my sound hardware info:

00:14.2 Audio device [0403]: ATI Technologies Inc SBx00 Azalia (Intel HDA) 
[1002:4383]
        Subsystem: Biostar Microtech Int'l Corp Device [1565:820f]
        Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- 
Stepping- SERR- FastB2B- DisINTx-
        Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=slow >TAbort- <TAbort- 
<MAbort- >SERR- <PERR- INTx-
        Latency: 64, Cache Line Size: 64 bytes
        Interrupt: pin ? routed to IRQ 16
        Region 0: Memory at f9ff4000 (64-bit, non-prefetchable) [size=16K]
        Capabilities: [50] Power Management version 2
                Flags: PMEClk- DSI- D1- D2- AuxCurrent=55mA 
PME(D0+,D1-,D2-,D3hot+,D3cold+)
                Status: D0 PME-Enable- DSel=0 DScale=0 PME-
        Kernel driver in use: HDA Intel
        Kernel modules: snd-hda-intel

-- 
ALC662, SBx00 Azalia Intel HDA, Alsa 1.0.22.1, Line-In and Mics not captured
https://bugs.launchpad.net/bugs/523953
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