DFS replication issues

[tom333]

Experiencing a really irritating problem with DFS replication. We use storage craft server edition to back up our file servers however this stops the DFSR service while running a backup. Normally this is fine however on this particular sever, the service fails to stop (default is 30 seconds, have set the time out to 5 minutes in the registry) and then gets killed (default is 20 seconds but i have changed this to 5 minutes also) which results in the DFSR database being shutdown uncleanly and in turn has to redo the initial replication. This happens every time the backup runs and causes data to become inconsistant.

Any ideas how to fix this?