I ended up building my own kernel using make-kpkg and stock Linux 2.6.29.4, with the .config from /boot/config-2.6.28-3-rt. No lockups in several days now, so whatever issue I was having is fixed in at least 2.6.29.4. I have not tested latency with this kernel, so I'm not sure how well it performs in regards to software running RT.
I ended up building my own kernel using make-kpkg and stock Linux 2.6.29.4, with the .config from /boot/config- 2.6.28- 3-rt. No lockups in several days now, so whatever issue I was having is fixed in at least 2.6.29.4. I have not tested latency with this kernel, so I'm not sure how well it performs in regards to software running RT.