Highlighted by Ars Technica, the issue applies to both early 2009 and late 2009 Mac Pro models. When playing audio through iTunes or a number of other applications, users have seen CPU temperatures double, while performance can take a serious hit.
Various user test have found that running Windows 7 via Boot Camp eliminates the issue, leading some to believe the issue is related to power management kernel extensions in Mac OS X.
"Further tests using benchmarks that run the CPU to full utilization show less dramatic temperature increases and, despite the high heat during audio playback, the Mac Pro's fans do not come on," the report said. "Confounding the issue even more is the fact that using audio doesn't seem to show any corresponding increase in processor load, just increases in power draw and heat."
Users have reported attempts to discuss the issue with AppleCare representatives, but have allegedly been told that the temperature range for the processor is considered "normal." Speculation on what could cause the issue from a variety of sources is available in the full article at Ars Technica.
Recent reports have suggested Intel's new six-core "Gulftown" processor could be headed to the Mac Pro in a future upgrade. Apple could stick with the workstation-focused Xeon line of chips, though some rumors have suggested Apple could switch to the new Core i7-980X processor, based on the same architecture.