eide:
...250 affiliates is very small amount - but switching affiliate solution is really pain in the ***. And costs a lot.
Yes it can be a pain - even more so for your affiliates at that point.
Do your homework and pick the one that's best for you from the beginning. There is no "best" in the market as far as features go - each seems to have some that others don't. Other intangible factors to look at include support and reputation.
Also, the market is quite fragmented. There's even some affiliate software vendors without an affiliate programme - go figure :)
Post Affiliate Pro supports tracks with use of Flash cookies, 1st and 3rd party cookies and IP tracking to ensure affiliates are credited with as little "leakage" as possible.
Regards
Peter