Very sorry for the delay. We'll have the updated release(s) for 2.5.5 and 2.5.6 out within the next week. There were some minor issues with this new release from Joomla. Honestly, the 2.5.4 check should check most of the really important (and commonly hacked) files. I'd start there and see if that doesn't report too many false-positives.
Never fun being hacked, we understand, and again, sorry for the delay.
Thanks,
Alex