You can try setting TIMEOUTALL 900 in your options file. This may alleviate the problem of licenses not getting checked back in after the application is closed. What is not supported in PADS is an idle state in the application triggering a license check in. If an application is closed and there are no network connectivity issues at the time, the licenses should be checked in.
Try the TIMEOUTALL setting. I may at least force them to be checked in after 15 min of closing the application.
Guy