I recently ran into a problem using AstroImageJ (AIJ) for analyzing AAVSOnet FITS images. The problem occurred while doing photometry on an image sequence. Values from the first image in the sequence impacted the results of later images, most obviously the max ADU or Peak_T1, Peak_C2,... Other photometric results also appeared altered. This does not occur if you do photometry on a single image unless you open subsequent images in the same window as another image.
You can work around this by doing single image photometry and always opening images in a new window. I also found that you can rewrite the AAVSOnet images with a simple python script and they work okay. This seems to result from the unusual image data scaling AAVSOnet uses triggering some defect in AIJ. The python code writes out the new FITS files with 32 bit data and no scaling. The sort of python code is shown here:
from astropy.io import fits
infile='blahblah.fts'
outfile='moreblah.fts'
hdu1 = fits.open(infile)
hdu = hdu1[0]
hdu.data[0,0]
hdu.writeto(outfile)
The AIJ developers are aware of this issue and see the same results that I do. The issue will be corrected, but might take some time. If you are interested in the details see this topic on the AIJ forum.
regards,
Cliff