I don’t know why anyone would create an affiliate tracking program, as a prerequisite to launching an affiliate program when there are at least a dozen established networks, with 1000s of affiliates looking for offers. The small and midsize programs can get you started for $1000 out of pocket.
Creating your own software seems like a reasonable goal, if you have an Aff program and you find problems that can’t be solved with a custom solution. The advantage of a 3rd party is that 1) they have 1000s of potential affliates waiting for new programs. 2) with all the accusations of shaving/dirty dealing here, working thru a 3rd party shoul help your program’s transparency.