It's been over an year already and the problem persists. It seems like it doesn't go without saying that 3rd party programs and fiddling with register are not solutions - they are workarounds. What we need is a patch from Microsoft. The problem is hotkeys disappearing; the solution is hotkeys not disappearing. Everything else is a workaround, and only Microsoft can fix this definitely.
I won't be following this thread anymore, but I hope to see a useful update in the near future.