I just had the following problem:
I pressed F6 to rename a method. In the Rename dialog the "Search in
Comments..." check box was checked. I entered the new name and pressed
Resharper opened another dialog because it found the method name in some
comments. I looked through the list and unchecked all of the
occurrences, then clicked continue.
Resharper renamed all the method names in the comments even though I
unchecked them. After undo and testing again, I found that it does not
matter how many occurrences I uncheck, it renames them anyway.
I don't know if this is reproduceable at your site, but it is on my
project. I just downloaded the latest bugfix 250 and it did it again.