Different WU's process at different rates, irrespective of the number of proteins, etc. Some of it has to do with whether the WU is compressed or optimized. I believe that has something to do with how many times it has been run through the process, once they begin getting similar data back on certain ones, they can speed up the process. One of my PCs has been crunching on one WU for about 5 days now.
Also, you might want to power the G4 down and then back up to see if that helps, just wait for it to finish a frame and write it, so you don't lose the last hour or so's work.
It's been about 18 months, since I even looked at a mac, but there is a built in sysinfo utility (somewhere), that will tell you what processes are running, and how much CPU they are consuming.
My G4 Powerbook started getting real sluggish, the fan stayed on all the time, and CPU utilization was maxed out.
Turned out to be the McAfee Anti-Virus. It had become corrupt, would launch, and then forever more, take up 75% of the cpu, forever.
Perhaps someone more knowledgeable about Macs can be more specific, but I think that this is probably the case.