Just chiming in here to say that this thread has helped me to fix the same problem of thumbnail alignment.
Turns out some of my thumbnails were 150x149 when they should have been 150x150. All of these wrong sized thumbs were ones that I had edited using the thumbnail edit feature in the gallery management area.
It can be really tricky to get an edited thumbnail to be the absolute correct size sometimes. This may be a bug in the thumb editor (or not) but, it would be very helpful it there was some way to either verify the thumbsize in the editor, or a routine in the editor that force corrects the edited thumbnail size to the constraints of the dimensions selected in the gallery options.
This weird alignment issue has been "bugging" me for months now. Other solutions offered included setting a number in the column field in the gallery options. This is a kludge work around that does help - but leads to issues with gallery thumbnail displays on small screen devices like iPhones and tablets, etc.
It would be really great to be able to bring this to the attention of the new developers as a "bug", or something that needs refinement - but I can't find a way to report it right now...
Again, thanks for this very helpful thread :-)