If you can get the problem to occur every time you build the current version of your program, I think it would be a good idea to report the problem to HP support and send your example to them. I think that even though it is happening on S-series, they probably would want to know about it and fix it. I imagine they still want to be able to verify the integrity of object files that they deliver for S-series systems, and if the fingerprint is changing for your program, it might change for one of theirs, too.
I don't know anything about running programs from xpnet, so it might be that ACI does something to the object file that changes the fingerprint, though I don't know why they would do so. If it is possible to build, fingerprint, run directly from TACL, check fingerprint and see a fingerprint change, I think that would rule out the possibility that ACI changed the object file. If the fingerprint changes only when the program is run from xpnet, then I guess you should contact ACI support rather than HP support.
I don't know the low-level details of how SWID operates, but I believe it is intended only to look at things in the object file that are directly related to how the program operates when it is run -- its code and initial data. So this change of fingerprint could be a sign that something is modifying the object file in a way that could change how the program operates. It is probably an accident, but whether accidental or intentional, if it changes how the program operates, that definitely is something undesirable and should be tracked down and fixed.
I hope I'm not being alarmist here and forgetting some benign changes that will trigger a fingerprint change. Assuming I'm right and the fingerprint change is as serious a matter as I think it is, you probably ought to get ACI or HP to investigate until they find out why it is happening and fix it.