Does FIPS 140-2 crypto certification matter for Bitcoin? I'm implementing part of the Bitcoin client in C# and noticed that I have the choice between FIPS 140-2 and non certified versions of SHA256.  Supposedly both versions give the same hash.

Does the choice of SHA-2 library matter for Bitcoin?  Does the FIPS-2 library exist in Mono and mobile devices?
You should basically never choose FIPS-140 unless you have no choice. FIPS-140 compliance is provided primarily for people who must comply with FIPS-140 for regulatory or policy reasons.

Note that that's not to say FIPS-140 validation is bad. It's great. If it finds bugs or problems, that's a pure win. If you have a choice between an implementation that has been FIPS validated and one that has not, the former is the better choice. But that has nothing to do with whether you enable FIPS-140 modes.

Your implementation has been FIPS validated. Don't brain damage it.