I had this issue on my Notes mail servers which were also SAN media servers. Anti-virus software was locking the files. The best solution I found was to use the following:
1) Removed the file extension from the anti-virus scanning.
2) Changed from VSP to VSS (Windows 2003 shadow copying) . This is set on the master server - ensure that when you add in the server name to the client attributes section under host properties - master server that you use the same case (ie upper or lower case) as the server name as in the list of clients or it won't work.
3) Set a disk limit of 1GB in Windows for the maximum shadow copy file size - system properties - advanced I think.
Not in work now so can't give exact instructions. If you need more clarification let me know and I can go through it step by step tomorrow.
The rationale behind this action was that generally VSS provides quicker and more reliable shadow copying with the added benefit that you can limit the amount of space used so the server shouldn't be negatively impacted on the disk space or performance side.