Anything like this?

I never did figure out what the problem was with mine. It was my Mk2 backup. Once I got my Mk2a back from Mark, I swapped the drives in and the problem was gone. Maybe it was something on the Mk2 board (ide) or maybe it was the lower amount of RAM (more likely). My problem was likely do to not enough RAM with my database size to allow for proper cacheing, yours (like you suspect) may be due to a bug that doesn't get full use of your RAM.

Didn't Mark post that 2.01 had trouble detecting added RAM in some situations? I think he added a workaround in HiJack to address this.

Your reboot problem is odd...