[This may be related to #3600221 and/or #3600569 but those descriptions didn't sound the same as what I experience.]
Windows 7 64-bit SP1. Similar to #3600221, I have confirmed that the issue DOES NOT occur with Notepad++ 6.2. It does occur consistently under Notepad++ 6.2.2.
After invoking compare (menu or hotkey), the language recognition is lost and the text is treated as "Normal text". Closing compare, I have to select some other language and then re-select the correct language to get the highlighting back.