I see the same high cpu usage and similar problems using the latest versions under Mac OSX Snow Leopard.
I opened Activity Monitor and looked and it seems that the main calibre.app seems to be running under Rosseta (PowerPC) on my Intel Mac while all of the calibre-parallel threads are Intel Native.
Under Snow Leopard, it no longer gives me the option to disable or enable Rosetta for the calibre.app so I could not change this.
When a conversion is done using the gui, a new thread (running) intel is spawned (but none of the calibre-parallel threads are used) and this new calibre intel thread sucks up 100% cpu for a long time.
So somehow, I think this problem is caused by the universal binaries and the use of Rosseta (the PowerPC code conversion)
I keep Rosseta installed because I need to still use the PowerPC version of Microsoft Office 2004 to get full Macro support.
Any ideas here, how I go about forcing calibre.app to run as a native Intel program on my Mac as opposed to running in Rosseta (PowerPC).