Ipe can pose a finishing problem due to it's oilyness. Sounds like your contractor used a wax free shellac sealer which should have worked if he applied it right after the final sanding, before the oils in the wood had a chance to rise to the surface. I would not have used 2 coats of sealer however. I would have also wiped the floor down well with acetone prior to sealing to help remove any oils on the floor. Then applied 1 coat of wax free shellac by Parks or Zinsser. After drying about one hour or so, I then would have applied the first coat of poly and allowed that to dry overnight. Come in the next day, screen, vacuum and apply the final coat. This should have worked. Another option with Ipe is to use a penetrating tung oil finish called Waterlox. It looks great on most floors and seals well. Will require a different maintainence shedule than poly will however. You also could post your question on this board, Floormasters.com It has a message board like this one with a lot of talented finishers.
http://www.floormasters.com/community/v ... 4eb2633f0e