RemoteApp application freezes

We publish an application through MS RemoteApp/terminal services windows 2008.  For a while we were having some users files stop responding durning login.  Soon found out it was because the off-site backup window was running too long and locking the files.  Recently it is happen again but only on a certain file and not due to back up window.  Basically the app minimizes and stays there unresponsive.  If I rename the user file and make a new copy of it the problem goes away so it must be file locks or something.  I have run net file but it doesn't report anything.  Ideas?
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Malware? Try doing a scan.
NET FILE lists remotely opened files. Use Process Explorer from Sysinternals. The Find feature allows you to search for a file. If this file is listed, it means it is used by a process.

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Windows Server 2003

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