This may be a stab in the dark. But the forge version of Dynmap uses DIM_MYSTXX_XX where X is the ID. (DIM_MYST11_11)
It's probably a Dynmap only thing but it's worth a try.
I can't believe I didn't test that, I do the YMLs manually, so I'm not bPermssions command friendly. Anyways, yes I do get a complaining error. Which leads me to believe the error stems from either Mystcraft of bPermissions. You know, back were I started. I'm just really bothered by the fact that bPerm's works with all other mod dimensions aside from mystcraft. And on the same note, I'm very hesitant about switching over to PEX after some of the reviews I read. More specifically a google docs article.
And while this isn't directed at me, I would like to reply to this. While I would "love" to be on 1.6.2 (sarcasm) I have to wait for all the mods to update before I can actually bump up to that version. The last I checked (about a week ago) I was missing nearly 50 mods, at which point I gave up. (The woes of having a custom modpack.) I do not mind having a few lacking mods but at this point I would of been missing important world generation. So thus, I'm forced to be stuck with 1.5.2.
You can use Essentials' /getpos or /whois commands to verify what the name of the world they're in is called according to Bukkit. When I had this problem I verified that the name of the world I was using was correct, but bPermissions was still unable to detect that the world was loaded.
I also could select world_twilightforest no problem, but selecting any Mystcraft age would not work. I too tried to chunkload the ages on startup, but to no avail. If PEX has found a way around the problem (and no other permissions plugin will work ) you might be best to use PEX instead. A working plugin beats a non-functioning one, after all.
Let me know how you get on, because I'll probably need to face this problem when I update to 1.6.2.