The fact that your proc jumps up that much is a decent sign. It more than likely means your process is not contending with any other processes for time on the proc. What I would be interested in seeing is the output from a vmstat 5 10. One prior to initating the process and another while the processes are running.

Without really looking into it too much, I want to point a finger at the I/O subsystem. I recently had similar problems with system utilities on a particular host. Come to find out the RAID controller was flaky. I couldn't see much of an issue, but it was the only thing I hadnt tested. So the disks got moved off of the hardware based controller, and ported over to software RAID. Viola the issue went away.

Its not much without a more fine tuned analysis of your particular system, but its another place to look. Seeing as how the same code runs flawlessly on a different host, it is on initial assumption more than likely hardware based. Another alternative route looking at a software level would be to use the 'strace' program to watch what is actually happening during runtime on that host. Its not the easiest tool to use at a 'junior' level, but will give great insights into whats going on.