I had the same problem with my 6 month old 2007 4wd 4-runner. I had a bad charcoal canister, and the dealer told me the VSC lights always come on with the check engine light, but implied that the VSC still works... I assured them that as of the snow storm the other day, the VSC was not working.

They could not explain why the VSC is disabled when the check engine light comes on. Sounds dumb to me ...

But I found another reference:

A detected engine problem could mean many things, so Toyota decided to kill anything that could be an additional load on the engine including the VSC system since it causes braking (the ABS does still work though).

I still call the VSC system a safety system and think it was a dumb move, but it at least makes a little sense.