Windows other than the current source window have their font sizes increased to that of the source code when presentation mode is selected. When presentation mode is exited, these lower and side windows are then shown with large fonts. Closing and reopening them seems to clear it up in most cases. Ones which are commonly affected are Changes, Favorites, Commander and Ant Build. Some tool windows are immune to this, such as Project, Terminal and Structure. Some windows, like Favorites and Changes, cannot be returned to their normal state without closing and reopening IntelliJ. This appears to be a cosmetic issue; everything still functions correctly.
I am using 13.1 EAP.