I experienced this too, are you guys using any external program that could write to those file and possibly reload them like mslDev or others external editor? It started happening with this change I think:
Originally Posted By: 7.31
7.Changed the "File changed" dialog so that it is closed automatically if a load/reload command applies to the same file.

In my case the file didn't change either, and it would happen randomly, I think it's a bug with mIRC.

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