Sometimes Rapid marks a file as changed (by displaying the asterisk in the file's tab) even though it has not been changed. This means closing the file requires dismissing the file save dialog, which pops up if a file has been changed.
I'm not sure how this state is achieved or whether it is something in particular files that causes the problems. Here is what I have noticed.
I open a file normally and Rapid does not indicate it has changed. I place the cursor in the file or make a text selection and Rapid marks the file as changed even though nothing has actually changed. Then I close the file, telling Rapid not to save the file. The next time I open the file it is marked changed upon opening, without my having taken any action at all.
Through experimentation, I found this workaround. I open a file that I know Rapid will mark as changed. I then place the cursor at the very top, before the first character. I then close the file without saving it. When I open it again, rapid does not show the file as changed.
I do not think this happens with every file and I suspect there is something about certain files that causes the problem. I cannot duplicate this problem with any file. I can reproduce the problem because I know of a few files for which this problem always occurs.