I have heard about this problem somewhere else too. The advice given was to inflate the tubes first to approximately 80% then before inflating the floor lift it at the sides and centre the keel. Then inflate the floor/keel again to 80%, then fully inflate the tubes and keel to full pressure. Reinflating to full pressure after 10/15 mins on the water.
Having said that I have had no problem with keel alignment on my Zodiac (I also use an electric pump similar to the Bravo) but maybe worth a try for you. Good luck.