A friend of mine had a late model Commodore SS, manual. It would not go into gear properly. The Holden dealer gave a quote on a gearbox rebuid, so my friend just parked it for a month. Then decided to have a look. Turns out there were a few rocks just sitting on top of the gear stick, problem fixed. I got all proud and told him "that could never happen on a Toyota, because there would be a rubber boot there or something"... but you never know.

I say, if the problem has fixed itself, it must have been a stone or metal burr somewhere preventing full gear selection.