Interesting to hear this. I use Logic 5.5.1 and also once had a problem with some disappearing VST plugins. I solved it by uninstalling some unwanted ones, but I never systematically worked out the nature of the problem.
I suspect this is one of the many bugs in Logic 5.5.1 (the "interpret lots of RAM as no RAM" being another I might mention...) that, alas, will now never be fixed.
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