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Strange. If you open the Tools->Options->Debugging dialog in Visual Studio, is the "Require source files to exactly match the original version" item checked? If it is not checked, that may cause it to use an old source file in the debugger.
As far as I know, the PDB age is part of the symbol file's unique identifier - when Visual Studio asks for symbols, it makes a request to a URL with the PDB GUID and age. I think age normally gets incremented when a project is rebuilt in Visual Studio, though I don't know the rules about this for sure.
Since you get the correct symbols/source if you clear out the symbol directory, I'm guessing Visual Studio just isn't making a request to ProGet because it thinks it already has the correct files. The best thing to do in this case is to run Fiddler and capture a trace of both behaviors and see what's different. You can send us a copy of these to support at inedo.com if you want some help troubleshooting.