Couple things you can check:
1) If you are bridging the amp, is the impediance the same output that the subs are said to run best at?
2) Could your amp be rated at 200W X2 peak? If it's peak, then you are realy only running 50W at each speaker, which may be less than you anticipated.
3) Sounds silly, but when you hooked it up, one speaker might have the negative in the positive clamp. This would cause the sound waves to sort of cancel each other out, and possibly sound quieter than it should.
Hope any of these ideas help.