Generally, the problem lies either in the synchro gears, or the locking collar that mates the gear to the layshaft. The root cause is generally abuse.

In terms of whether or not to rebuild your tranny:

While a used tranny is cheaper in terms of initial outlay, it is always a gamble. You could wind up with a dud tranny. A rebuild, OTOh will be as certain a solution as one can get. So if you're planning to keep the car for another eight to ten years, I'd spend the money on a rebuild, and have the comfort of knowing the tranny is truly fixed.