We use a good script for the keyaudioads affiliate program. It's not perfect but it will certainly do what you are wanting. Their support is excellent. Its post affiliate pro 4.
We've had to do a little custom tweaking with the code to get it to do things specifically for our program, but for value for money, it's pretty good.
We needed to display custom JavaScript snippet for our members.
Because we pay our affiliates for every audio ad they play on their websites, we needed a fix for that and a way to track the plays. Thats what we had to tweak.
But as majority of aff programs are ppc or pay per lead, sale etc, thats what they cater for.
You get a 30 day guarantee anyway, so you could try it out
We've also used Post Affiliate Pro and recommend it, not had any tech issues in the last few years, so hopefully you can resolve it.
Otherwise what about joining a small affiliate network? They handle the tracking and payment for you, plus fraud detection etc. Given the current climate you might be able to strike a good deal with some of the smaller ones. Perhaps paidonresults, shareasale etc. Good luck
went with pap and after getting it installed - not helped with installing the latest version followed to 2 updates in a week - it looks OK
Are the updates as fast & furious as this usually?
(Bearing in mind I have had to twice go round and tightened all the virtaul bolts...)
Answer = yes - I have never knownn software have so many updates - Its getting to be almost twice a week - and everytime I have to go around and make the templates good again