When I run a time series, not all of the image data appears in the AAVSO file to upload. I ran a time series for Aug 11 - Oct 31 for the V values on RS Sge and it looks like about 10 of 66 files didn't make it in. When I ran a series for R, only about 15 of 66 made it in. I thought it might be that the data had already been uploaded to the AAVSO, but this is not the case in either series. Something I am missing?
Is the target very faint? If so, it could be that the minimum SNR requirement will make VPHOT skip some images. The default is SNR > 20, meaning that images where the target has SNR less than 20 will be skipped.
You can change the default on the start page of the time series analysis. Set it to 1 or something if you want to force all images to be analysed.