That's indeed weird.
The best thing you can do: when the problem occurs again, see what you've done/changed between the last time you've run Reaper without problems and this time, where Reaper has these problems.
Oh, and you could build in a check in your __startup.lua. Every time NamedCommandLookup returns 0, although it should return something else, pop up a message:
reaper.MB("Here we go again: The Bug has returned!", "A Bug's Life", 0)
This should give you an indicator to when the problem rearrives.
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