We just upgraded from moodle 2.5 to 2.6 and the labels in several courses have started behving very differently. When the side columns are docked the labels no longer stack they start to appear side by side. They are also all formatted as gray with white text, I have no way to change that. Is this a new look as this seems to persist across several themes.
This is just a guess, but as of 2.6, the default install theme is bootstrap which uses clean. These themes usually act as parent themes for many of the other themes that are standard in Moodle and other custom themes tend to use these as reference. It might be that the theme you are using (a custom one?) is taking some clues (CSS?) from one of these underlying themes and they are affecting your theme in a negative way. There have been a lot of changes to these themes for 2.6, as well as a change (I believe) in the underlying Yahoo libraries that control them. Do you get the same issues with one of the core themes?