there can be a few reasons for such waves:
1. a spherical pano with too low details settings,
have a look for every details setting in every xml, it can be also set for a <level> node,
2. a cubical pano without Flash10 (krpano 1.0.7 or lower) and low details setting
3. a cubical pano with Flash10 low details setting and enabled fisheye effect,
Flash needs to split the image into many small parts for correct 3D displaying,
the more parts the more accurate, this is controlled with the details setting,
only with Flash10 (krpano 1.0.8) and cubical panos, this splitting is not needed,
then the image should be perfect,
try downloading here to latest tool version:
http://krpano.com/download/beta/
and convert the pano first to a cubical with the SPHERE to CUBE droplet,
and then drop the converted 6 sides onto the kmakemultires droplet,
then there shouldn't be any waves/ripples anymore
best regards,
Klaus