I've got the same issue. I don't use Hibernate, but I've noticed when I'm playing music and I shut down using the power button inside RR, it doesn't save my spot where I've been playing music and when I start up RR again, its all the way back where I was first playing my music last time - it's a bit annoying I must say as I always play the same song every time I start RR.
And like you said, if I shut down RR and exit it completely, it does save the resume spot correctly.
I'm using the latest Oct (11?) 2008 build of RR.