I wonder if this is related to the script since we started seeing it sometime after the script was installed for both of us.
It might actually be due to something in the WME code that is not available anymore when the script tries to reference it, like an incomplete layer or object that was unloaded.
I use a hacked (modified) version of the script that has one or two extra features in, and have not had the greyed buttons. I somehow would live with the buttons rather than miss what the script reveals.
What could help in identifying the possible issue is looking at the Chrome error log when you notice the buttons went flaky. It might give Tim an idea what to look for or where to look if it is the script.
It might be that he just needs to bulletproof a portion of the code to accommodate a flaky WME session.