Hi,
As any standard, the FITS standard is open to interpretation and erroneous implementations (by other programs...). There quite a few posts on the issue of FITS file reading in the PI forums.
To make things short, the problem is usually due to either an erroneous FITS header (for example BZERO is wrong), a file with data that does not match the header or the use of floating point data. Some of it can be rescued by setting some options in the FITS file format.
I have hacked a small script (attached) that dump the header of a FITS file to a text file (of the same name, in the same directory, with extension txt). It does not use the PI image load, but directly read the files. You should be able to read the header of one of your problematic files and post it here. Surely somebody can then help you.
-- bitli