So I was struggling through some issues with my scanner when google turned up this thread (summary: the usb stack in 2.6.11.x is fucked). Sure enough, upgrading to 2.6.12 fixed the problem (and I probably my gphoto related camera issue, although I haven't confirmed it yet)...
After upgrading, I discovered this blog entry and learned that the kernel realtime lsm has been deprecated in favor of the set_rtlimit program. The good news is that set_rtlimit with 2.6.12 seems to be working beautifully! I'm running jackd and pd each with a priority of 30 and haven't been able to see any xruns! In fact, it's working way tighter than the previous setup. Rawk.
The downside to all this is that jackd is completely clusterfucked in Debian unstable at the moment. I dist-upgraded as part of my earlier troubleshooting, so now I'm stuck with a bit of dependency hell until the package maintainers get caught up. Fun.
It might be a little early to tell, but it also looks like the upgrade to 2.6.12 fixed the regular gkrellm crash I was seeing, which is cool, cuz it was bugging the hell outta me.