Just to clarify, are you saying that you highlight the object it found as being different, and the differences pane at the bottom shows nothing highlighted?
If so, I've seen this kind of thing occur before where the only difference is in something like the carriage return type in the extended properties text (i.e. the DB has a CR, the other db (or script file if comparing to scripts) has a CRLF. Because these characters are invisible, nothing gets highlighted.
You can narrow down what the difference is by ticking some of the ignore options- for instance ticking the option to ignore Extended Properties will then treat the objects as identical (assuming the only diff is in those)