I guess if you're using Shimano the bottom bracket installed is Octalink. FSA offers both Octalink and Isis type crankset so there should be no issue. Though you need to check on the chainring. I know of some issues on the chainring difference. FSA offers compact (50-34 and 52-36) chainrings which might pose problem if your using shimano FD. The differential limit on shimano (not sure) is 14.
I've been using a FSA 52-36 and Dura Ace FD, at 4000 km so far no problem for me. It took quite a number of tuning and testing before getting it to work properly.
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