Do the file sizes and the date/time stamps on the application PBD's/DLL's get updated when the update/distribution process runs?
Is the server configured as a failover primary/secondary or replicated server pair?
We have one customer that utilizes these for their production, user acceptance test, and test environments. When they install an update to their production servers, for example, they must copy the new files to BOTH of the replicated servers, because if they update files only on the server that is currently inactive, the users will not see any updated files. This sounds like what is happening in your case - but I'm not a Server Administrator, so this is purely a guess at this point.
Does this issue happen with any other applications that are installed and made available on the same server(s)?
There has to be something else going on that you may not be aware of and have not told us about. You may need to work with your Network and/or Server Admin's to troubleshoot this issue further, because it does not appear to be a PowerBuilder-related issue.
Best regards, John