Any time you sign onto PSN with a CFW you run the risk of being banned, especially if you have run homebrew software on that PS3 (such as an emulator, MultiMan, etc.). Fortunately there are some useful tools you can download to minimize the chances of being banned. PSNinja, PSN Patch, PS Nope, and a few others can delete your game launch history and disable CFW calls making it more or less impossible for detecting homebrew and CFW. Nothing is guaranteed but if you sign onto PSN without taking the necessary steps to cover your tracks your PSN account and Console ID will eventually be banned from PSN. I use a combination of PSNinja and PSN Patch prior to signing onto PSN - PSNinja provides a quick and easy way to delete your game launch history and PSN Patch can be used to disable CFW calls before you sign onto PSN.
Sign out of PSN before running homebrew software, or take it one step further and disconnect from the network and run your homebrew while offline.