I am using version 2.3.1. I have a fairly decent computer; AMD x2 2.7ghz, 4gb ram, Ati HD3870. I never had this problem in xp x64 or x86, and now that I "upgraded" to Vista Ultimate x64, I have this problem. I'm thinking that this might be a problem with Vista's networking rather than a problem with fahmon, but I'm posting this here all the same.
Anyway, if I have fahmon open (can either be minimized or maximized) and am playing a game (Team Fortress 2), every time fahmon polls all of the clients in the list, my fps drops from a solid 60 to 10. It'll bounce back and forth rapidly between 60 and ~10 for maybe 15-20 seconds: until all of the clients are updated. Closing fahmon eliminates the problem.