Similar problem and had Adobe response (still a problem though)
This isn't an answer but may help you identify the problem.
In Dreamweaver CC every time I switched apps (away from DWCC) the open file reset itself as if it was just opened again losing all changes. Contacted Adobe and they told me to switch on the View History display to see what was happening. Every time I switched out of Dreamweaver to another app Dreamweaver reset the history completely. Adobe got me to reset preferences (http://helpx.adobe.com/dreamweaver/kb/restore-preferences-dreamweaver- cs4-cs5.html). When repeated after reset I got the same pop-up fiel changed message that you were getting. Appears that I must have clicked the check box to dismiss the message and that sets it at YES refresh the document if this problem occurs again.
Adobe's said the message can't be set to automatically be set at NO i.e. don't reload but dismiss the pop-up. So now I get this pop-up all the time if I switch from DWCC to another app and when I go back I need to click NO.
When I asked Adobe how to trace what was causing this, they closed the support ticket saying 'file changed outside of DWCC' i.e. 'not our fault'.
My files for this job are stored on a network server and no-one else is using them except me so I'm the only one that changes them. If I store the files locally and edit/switch apps then I don't get the message. So I am assuming that it is some file time/date stamp comparison that DWCC is making between what is in memory and what is on the server and for some reason the discrepancy is too great so it flags as changed. Or the server is doing an automatic save which is setting the changed flag on the file so again DWCC thinks it's changed.
I've no idea how to test or how I could change DWCC to stop doing this and Adobe have decided that it's my problem not theirs - which it probably is - but it would have been nice of them to advise on how to check :0) I can't believe I'm (and you) the only one experiencing this (and if you search for this message you get results going back to 2003 with the same problem on DW)
Hope this helps you to identify your problem as I assume it's the same process/logic in Adobe that is causing this.
I have created a support ticket so we can look into this issue further.
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If anyone else is experiencing this same issue, please append to this thread.