I am having similar problems with the latest PM version. I used the apply rotation command, {alt}R, on several selected photos, but it only appears to work on one. The soft rotation indicators are still on in some of the selected photos. If I go back to select and correct one photo, those previously selected are rotated a 2nd time. This may not be exactly what is happening since I can't figure out exactly what is going on. I've had to go back and apply rotation to each individual image until it is correct. I used to be able to select a group of photos that included both soft-rotated ones and non-rotated ones, apply rotation, {alt}R, and all the soft rotated ones were handled correctly. I did read in the release notes that something was done to the apply rotation command, but I am now unclear on how to use it now.