It does have separate home and car memory as you said, and your expected behavior is correct. It should not have done what you said it just did.
There are some known bugs in the 2.0b11 EQ, although that particular one hasn't been reported yet as far as I know. It is possible that it might be a bug in Hijack because the latest versions of hijack do in fact mess with the EQ.
It would be helpful if you could narrow down whether it's Hijack or whether it's 2.0b11 raw. Can anyone else help test this? Genixia, do you have any ideas?