Interesting. My first thought would be to check if there are hidden files somewhere in the old directory tree... If there are a large number of files in one directory, all sorts of directory operations can definitely slow down, and if they are hidden files, they might not be showing up in whatever method you are using to compare the trees. (And I am assuming the slowdown isn't due to build products accumulating somewhere... You have cleaned the builds and compared the full directory hierarchies?)
If they are really truly identical directories (including hidden files, subdirectories, etc.), then ... hmmm ... there are so many layers at which a slowdown might potentially occur. To try to narrow it down: How long as the VM been running for? Do you, for example, leave it running 24x7x365, or do you suspend it when you're done with it for a while and resume it next time you need it, or do you shut down the OS and boot it up when needed? Just trying to figure out which parts might be likely to have become "gummed up" so severely, and the list of possible culprits could depend a lot on how you use the VM.
In addition to what Darius says, check your antivirus settings.
You might want to consider excluding that network share from antivirus checks.
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Good catch - and it's possible that it's AV external to the VM as well, running on the NAS host, but only on one directory rather than another.