I has exactly same issue with FP3 its definitely buggy...
After install
1. Domino did not start "nsdhelp.dll" found "nsdhelp.dll.hf" renamed back to "nsdhelp.dll" domino started
2. No HTTP
3. Reinstalled "DOMINO_9.0.1_64_BIT_WIN_ENGLISH" applied patch FP3 "domino901FP3_w64"" This time FP3 did not gave warning"
Everything seems to be working.... on by 2012R2 box