It is quite possible that the files are in use, as the standard client-launched compact is a copy style compact. I would suggest a weekly or semi-weekly program document be setup to run during non-business hours. Set it up to compact all databases with more than 10% white space. Your program document would have a "-S 10" command line.
Dig Deeper on Lotus Notes Domino Mailbox Management
Related Q&A from Michael Lazar
Learn how to easily keep track of the numbers of incoming and outgoing Lotus Notes email messages to and from your Domino server each day. Continue Reading
Discover what steps you can take if your Lotus Domino server runs out of disk space and you have issues sending and receiving Lotus Notes email ... Continue Reading