You have synchronization rings between every gear and they wear independently of one another, but chances are in the past either you or the PO routinely abused that shift. Or it could be because those gears were used most frequently in its lifetime and it's just wore out. At 20 years old and a couple hundred thousand miles, it can be anyone's guess.
Sometimes they make noise and sometimes they don't, because sometimes they're working properly and sometimes they're struggling to keep the speeds matched. That's how a failing part behaves generally, sometimes it works fine and others it causes a problem which may seem fairly inconsistent. Chances are there's a common denominator out there but it's not readily apparent, and for all intents and purposes I'd say it's really not relevant anyways - they're not gonna magically get better if you deduce and avoid it, whatever it is
You can have synchros replaced but it's typically pretty pricey (trans has to be completely broken down) and it might benefit you to find a full on replacement from a junkayrd