here is something, i just got one of those vintage modified basses into the shop and the guys main complaint is that
i would drop it off and it would be set up and play like a dream for 2-3 days and then start buzzing and would not hold tune AT ALL!
(this is the third time its been in)
so last night im messing with it and i noticed that when i held it and played it was flat, but when i had it laying on the bench it was perfectly in tune.
then i noticed that it had a dreaded case of "cheap-neck-itus"
basically the soft maple fingerboard wasn't doing much for the truss rod.
i doubt thats the same thing that is going on with you(usually short scale necks are solid!)
but i figured i would throw that out there.