Heironymous,
Wow, another Dvorak user! I have not seen the problem you described. However, I have three mappings in my menu item in the menu bar: DV, DQ (Dvorak with Qwerty keyboard shortcuts) and US. Sometimes DQ disappears from the list and mysteriously comes back later. Overall I much prefer Mac's support for Dvorak over Windows - the switching back and forth works consistently on the Mac. At work I never switch back and forth anymore - I just refuse to let anyone type on my computer. At home on my Mac I switch to US when my fiance' uses the computer, and also when I play games like Warcraft III when I use left hand only on the keyboard. I used to use DQ because my Microsoft Internet Exploder mouse's driver and also Speech Commands got confused trying to execute keyboard shortcuts. The mouse has improved recently and I never use Speech Commands.
Even with these small annoyances, I'm addicted and I won't ever switch back to Qwerty on a regular basis even though switching back would be easy because like you said, it's like two languages - it just takes a few seconds to switch the brain circuits over.
So to all those silent masses secretly wondering: Is Dvorak worth the pain of switching? ---> Come, join the Dark Side. Together, we can rule the universe!