Server and build agent sources get out of sync about once every couple weeks using Clearcase

We use clearcase for version control (I know it is terrible, no option unfortunately as this is a big enterprise client that refuses to use anything else.)

Long story short is that every once in a while (every few weeks), the server and build agent get out of sync.  I try cleaning sources for all builds on the build agent and they still are out of sync.  I usually end up manually copying files from server over to build agent.  Any way to fix this reliably?  What could be causing this?

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