Thanks waterwingz!
The iso=100, shutter speed=1/2000, and ND filter='out' were set in the "enhanced photo operations" menu.
So it sounds like even though it was set to not drop the ND filter in, the camera still determined that it should use the ND filter(it was a very bright day), which resulted in the F9.0 (ND Filter In).
Is there a better way in CHDK to lock the ND filter out?