Hello Bob,
There is much more that goes into a successful affiliate program than just the software. Unless you already have a large and loyal fan base, you probably won't have a large enough audience to market your program to. Even then, the base that you are able to mobilize is probably not going to be very experienced with affiliate marketing. If your program succeeds despite these odds, then you still have to pay your affiliates and provide transparency.
I don't represent a 3rd party affiliate program, but have seen clients attempt in house programs versus 3rd party. A 3rd party (like Commission Junction or Share-A-Sale) program brings a market of existing affiliate marketers and can really improve your chance of success. Share-A-Sale, in particular, is very cost effective.
The other benefit is that they bring the software to the table
-Matt