Has anyone else experienced missing files and folders when using DFS-R and Kaspersky?

We were running Kaspersky and FRS together quite happily. With the intoduction of Server 2003 R2, we decided to switch to DFS-R for replication instead.
The result was that over this weekend, 30% of our files and folders disappeared (both ends) from the share using DFS-R.

Lots of errors in the logs about files being modifed on both servers and lots of files in DFSRPrivate\ConflictAndDeleted.

These errors were happening at 4am on Saturday morning with no users.

We are investigating both AV and backup (CommVault Galaxy) programs.

CommVault properly suspends DFS-R during backup, just like NT backup.