I actually had a web application that worked perfectly with CTRL keys, but then decided that I was smart and used the accesskey attribute, and ran into this exact problem with IE.
The problem with switching to CTRL shortcuts is that many of them are more standard / useful in many applications (for example: cut, copy, paste, select all).
Ctrl + Alt is quite safe, but requires more work with the user part.
I try to just try to stick with ALT shortcuts. IE does not stubbornly insist on appeal.
Successfully canceled CTRL + A / CTRL + F demo: http://jsfiddle.net/egJyT/
This answer seems to imply that it is not possible to disable menu shortcuts without putting IE in kiosk mode.
Kevin stricker
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