As a Dvorak user, ive had this problem (or similar ones) for years. I basically gave up typing in Dvorak on my windows machines (thankfully my primary desktop is Linux)
As a Dvorak user as well, I've found that as of Windows 10 (and perhaps 8 but I've not used that extensively), they've finally fixed their multiple layouts issue. You can disable the nonsense that is "different layouts for different windows" and get rid of the awful alt-shift abd ctrl-shift shortcuts and just switch layouts with win-space. I keep qwerty as a layout for when others need to use my laptop but the OS never unexpectedly switches me anymore. They finally caught up with classic MacOS lol
Same, I had this from years. Strange to see it here.