sounds like a poorly designed program, BUT... there are registry settings out there that keep the card in "warm standby" even with the 6700 "off" - I've posted links to them before, and posted them in the 2.2 rom thread as well... I can track them down - I've not needed any of these settings since going to 3.3 myself, but they may help in your case.
Edit:
Here's the link:
http://pdaphonehome.com/forums/ppc-6...stable-12.html
And these were the ones I was thinking of:
DSOD RELATED IMPROVMENTS
HKLM\Drivers\SDCARD\SDBusDriver
PowerUpPollingInterval - 2 (Dword)
PowerUpPollingTime - 2000 (Dword)
These settings we're borrowed from the Treo 700w.
HKLM\System\CurrentControlSet\Control\Power\States \Suspend
dsk1 - 2 (DWORD)
Prevents the SD Card from going into suspend; the main cause of DSOD
cam1 - 4 (DWORD)
Forces the camera to turn off during suspend, saving power.