I ran the following from /opt/scripts/tools for no good reason other than 
curiosity:
update_bootloader.sh
update_kernel.sh
update_initrd.sh

Now my BBB goes to 4 solid blue lights if there is a microsd inserted 
during bootup. With no sd inserted, it boots up fine.

Serial log with sd inserted:

U-Boot SPL 2014.10-rc2-00017-g621bc23 (Sep 04 2014 - 19:58:48)
reading args
spl_load_image_fat_os: error reading image args, err - -1
reading u-boot.img
reading u-boot.img


U-Boot 2014.10-rc2-00017-g621bc23 (Sep 04 2014 - 19:58:48), Build: 
jenkins-githu 
                                                                            
                                                                            
    b_Bootloader-Builder-22

       Watchdog enabled
I2C:   ready
DRAM:  512 MiB
MMC:   OMAP SD/MMC: 0, OMAP SD/MMC: 1
Using default environment

Net:   <ethaddr> not set. Validating first E-fuse MAC
cpsw, usb_ether
Hit any key to stop autoboot:  0
gpio: pin 53 (gpio 53) value is 1
switch to partitions #0, OK
mmc0 is current device
gpio: pin 54 (gpio 54) value is 1
SD/MMC found on device 0
Checking for: /uEnv.txt ...
Checking for: /boot.scr ...
Checking for: /boot/boot.scr ...
Checking for: /boot/uEnv.txt ...
** Invalid partition 2 **
** Invalid partition 3 **
** Invalid partition 4 **
** Invalid partition 5 **
** Invalid partition 6 **
** Invalid partition 7 **
gpio: pin 56 (gpio 56) value is 0
gpio: pin 55 (gpio 55) value is 0
gpio: pin 54 (gpio 54) value is 0
switch to partitions #0, OK
mmc1(part 0) is current device
gpio: pin 54 (gpio 54) value is 1
SD/MMC found on device 1
Checking for: /uEnv.txt ...
reading uEnv.txt
1757 bytes read in 7 ms (245.1 KiB/s)
gpio: pin 55 (gpio 55) value is 1
Loaded environment from uEnv.txt
Importing environment from mmc ...
Checking if uenvcmd is set ...
gpio: pin 56 (gpio 56) value is 1
Running uenvcmd ...
** Invalid partition 7 **
** Invalid partition 7 **
** Invalid partition 7 **
Bad Linux ARM zImage magic!
Checking if client_ip is set ...
Checking for: /boot.scr ...
Checking for: /boot/boot.scr ...
Checking for: /boot/uEnv.txt ...
** Invalid partition 3 **
** Invalid partition 4 **
** Invalid partition 5 **
** Invalid partition 6 **
** Invalid partition 7 **
## Error: "nandboot" not defined
U-Boot#

I can see it is obviously trying to boot off the sdcard and failing because 
there is no image on it. How can I fix this behavior an return it back no 
normal (so it won't try to boot off the sdcard without S2 pressed) without 
reinstalling the system image?

-- 
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