I have shot a few long exposures now (like 10's of minutes), and have found them to be noisier on average than a similar exposure on my 40d, but I usually run the long exposure NR on my 40d.

I haven't seen this on the 5d's custom functions - did I miss it, or do I need to do them manually?

With LR3's pp, the noise isn't an issue, but I'm curious.

Pretty sure that the 5D doesn't have it, but now that I think about it, I've never really looked.

are you doing lots of exposures back to back? Could you be overheating the sensor? I found this out the hard way.