My understanding of this message is that during saving or when saving was happening, a difference in files occurred. It means that when GM read the data to load in the program (usually project information) it was in one way and, before saving it checks if it changed. Therefore it gives you the choice: Do you want to save it the way it is in the IDE or do you want to load from the disk again and ignore what you've changed.
This can happen for many reasons. One is virus changing your files. Another is that your folder is syncing with something else, for example in another PC where another person is changing the files or even in a Dropbox folder. Another possibility is what happens to me, I usually do "double saves".
The double save problem is that I usually use the hotkey CTRL + S to save my project and scripts. But if you use it while GM is still saving your last "save" action (pressing CTRL + S twice), it may happen that some files were partially saved and some didn't finish saving, therefore the second save finds the data in a special case where it was partially changed. This message is not a real problem if you know why it may have happened. In my case, when I know that I double saved, I usually only press Save and my changes are re-saved, ignoring past states of the disk.
If this is happening to you every single second/minute or with any frequency, I advise you to backup your data and try to find the real motive for your disk data being re-written. As I already mentioned, sync programs like Dropbox, or network folder usually change the timestamp of "last modified" and may cause this. Although some data changing viruses or anti-viruses may also cause this to happen.
Well, that's my personal experience with this dialog and I hope I've helped you... If anyone else has another possible motive or knows something I said wrong here, please correct me