Are the files roughly the same size? The raw files you get from the camera are probably 16-bit integer (BITPIX=16). After calibration they may be floating point (BITPIX=-32) and it may be that Vphot can’t cope with that. The FP files will be twice the size of the integer ones. If Vphot can’t cope with FP that is a bit poor but there may be an option in ASTAP to save as ints.
I hit exactly that problem with Astrometrica. To solve it I wrote a Perl script to convert from floating point back to 16-bit unsigned integers. Not entirely trivial because a FP number can be negative and the range can be greater than supported in 16 bits, so off-setting and scaling was required.