Incredibly slow rendering in Media Encoder CS4 for Mac

We're having a strange problem trying to render a Premiere Pro CS4 project in Adobe Media Encoder . We're doing a 720p H.264 file that is about 35 minutes long. On my macbook pro laptop it took about 24 hours to render. As an aside, the same sequence and quality level in our previous editing method using avisynth and x264 only took about 2 hrs, but that's another story.
So, we figured we would bring in the big guns and render it on our 8-core mac pro desktop. Turns out it's estimating the render at 34 hours and the CPUs are 70% idle on average. So, what gives? What in the heck is wrong with Adobe Media Encoder that it is going even slower on our Mac Pro? We even copied all the files to our local 7200 RPM sata internal disc just in case the problem was due to a slow NAS device, but that didn't help it at all.
We've run all updates, so we're running on the latest version of the encoder.
Any ideas?

OK, here is an update. The original estimate for the single-disk setup was up to 75 hrs before we halted it. This is way slower than my laptop doing the same thing, so I think something is wrong.
We put in four separate 7200 RPM internal sata disks now: one for scratch files, one for video source #1, one for video source #2 (we have a sort of picture-in-picture thing going on on this video), and one for Premiere Pro to run from. Yet we're still seeing low CPU utilization and high time estimates.
Any ideas?

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