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I have been having a similar problem with real alternative 1.25 where it was setting the system wave volume to zero whenever I opened a real audio file.
That reg file from myie2user semi-cured the problem, but my wave volume was being set to 100% whenever I opened a real audio file.
I discovered that if you change the values from "100" to "-1" then you volume controls will be untouched when you open a file. Here's the reg file for you: