@jennifer_voorhee -
There's an FAQ about it:
Why am I having errors downloading from fanfiction.net?
Basically, ffnet (to the best of my knowledge) throttles based on number of network requests. Each chapter is a separate network request, so more chapters as well as more stories will hit those limits faster.
About the only thing you could change in FFF is the
user_agent setting, which may or may not help if set to masquerade as a regular browser. How to do that has been
discussed here before.