Is this a bug in genomestduio ?

The output of the GenomeStudio (.bsc) file, when it is opened after some time for reanalysis, is giving different call rates for some of the samples .264 samples, it was >95% when the analysis was done and the project was saved, later when the .bsc file is being used for re-analysis now, 18/264 are now <95%. I tried recalculating the same but then it is of no use if we do and save the analysis.

There is also a difference of call rates for some of the samples when it is analyzed array wise compared to the bulk analysis.

Is there some way to fix such that each time we do reanalysis we don't see in this change in the call rate?

Do let know your advice and input, it would be very helpful