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In most cases, this behaviour is caused by some corrupt messages within the PST.

When a PST fails to migrate using the Enterprise Vault PST migration tool, you should first run the Outlook feature Inbox Repair Tool called scanpst.exe. This can diagnose and repair errors in the file if you can't open your Personal Folders file (.pst) or Offline Folder file (.ost) file, or you suspect that your .pst or .ost data file is corrupt

scanpst.exe scans only the .pst or. ost file, making sure that the file structure is intact. It doesn't scan your mailbox on the Microsoft Exchange server.

scanpst.exe is installed when you install Microsoft Outlook and is located at:

drive:\Program Files\Common Files\System\Mapi\1033\

For detailed information about running the tool, see the Help file, scanpst.hlp, at the same location.

Note: Use scanost.exe, the OST integrity check tool, if you get error messages when you synchronize your .ost file with the Exchange server.
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Are you sure this isn't corrupt PSTs and the V6 upgrade is just a coincidence?

Oh yeah, and are these new type (Unicode - Outlook 2003) or old type PST format?

The PST files are old type. The other thing I forgot to mention is the same PST will import through the GUI without issue but will not import using evpm.

Doh! Important! Try SP1 if this doesn't fix it I think you will have to ring support as it looks like a bug. You can try copying evpm.exe from a ver 5 server but I can't reccomend this on live as I don't know enough about ver 6 and you might screw the import. Try it on your test environment maybe? If evpm.eve from 6.1 fails but evpm.exe from 5.5 works on the same PST file then it's a bug...

Let us know if you do ring support what they say.