sounds like its useing a different language layout to me. different region specific keyboards have slightly different layouts. like the _ and ? and a few others are swapped on american and england keyboards, even though everything else is still the same.
are you sure your using the correct region keyboard layout setting for the keyboard your using?
to check this, you first need to know what the keyboard layout is.
goto control panel, open the keyboard settings, and select the hardware tab. it probably will say what it is.
then goto the region and language settings in the control panal. select the keyboard tab and make sure that its set to use the correct language layout.
as for why its not showing correctly only in a few places, the keyboard might even be setup to use multiple language packs and thus IE is telling it to start useing a different one when its up for whatever reason. or theres a hotkey setup to switch between them that you don't know about