I guess that depends on what issues you mean.. I have a 2001 jp6 that's just great. Any guitar that old could have issues depending on what it's been through..
I have 2004 JP6, no issues whatsoever. Could easily say i like it way better than 2012 JP6 i own atm. Imho the pickups sound better, it has slightly fatter neck which i prefer and insane neck figuring... If its not beaten to death or has a broken neck or something like that u will be fine lol
I've got a 2001 JP6 and it feels just as good and as reliable as the current production models. I do happen to like the sound of the original custom-wound pickups more than the current pickups (which are higher output).
never underestimate the older EBMMs with the solid colours etc. I like them a lot, mostly more than the newer high end stuff with the figured tops and all that bling ;-)