Problem producing 360 equirectangular photospheres with Photomerge

I've been creating equirectangular photospheres from overlapping photos for Facebook etc using Microsoft ICE, but that, like Google Streetview, is prone to glitches in smaller environments.
I'm now trying Photomerge and would be pleased with the results - no noticeable glitches - but the resultant images have a wave in them. Is this a settings on creation problem? Can I correct after in anyway? It makes them unusable.
All suggestions greatly received!