Comparison Status Changes After Viewing Files
"I was comparing source code for two versions of our product. I found one file that shows in tree view as different. When I double click to compare them, it shows no difference. Then when I close that tab and come back to tree view, it shows them as the same."
By default a Folder Compare session uses a simple timestamp/size comparison because it is much faster than comparing file contents.
When you double-click the files, you open them in our Text Compare, which uses the File Formats to perform a rules-based comparison. (Note that unimportant (blue) changes will not show up if you have Ignore Unimportant Differences enabled.)
The rules-based comparison finds that the text in the two files is equivalent, and marks the files as equal. We then propagate this information back to the Folder Compare as the middle column: the black equal sign. If it finds the two files are different, we mark it as a red unequal sign.
By default, this will override the initial result of the quick test (timestamp/size comparison). This behavior is controlled by the Session | Session Settings | Comparison | Override Quick Test Results setting. If you uncheck this option, the black '=' will still be present but the quick test results will also help determine if the files are equal.
Alternatively, in the Comparison tab, you can also set the Folder Compare to perform a rules-based comparison on every file as you load the folders. Just enable the Compare Contents, and Rules-based Comparison options. This is also per-session or can be set as the default.
There are a few other reasons your files may appear the same, but Beyond Compare claims that they are Different, discussed here.