Lion runs slower than Snow Leopard

We called about our very new Power Mac with 12 cores. We are running Maple on that machine, and less than 2.4% of one CPU is used for our calculations in the Lion 10.7.4 windows mode. The last advisor advised us to install Snow Leopard on the new machine.  
We tried that as we had bought a family pack of MacOSX 10.6.3 some time ago and used that for two older machines. But the new machine complained that the installation can not be performed as this version apparently uses a fat binary.
We have also contacted Maplesoft, and they believe that Java and the GUI in Lion may cause the delay in the calculations. They advised us to run in Command Line mode using the nohup feature (In Terminal ending the UNIX command by &). We have tried this and found CPU use of 100% and even higher in parts where parallel processing was used. However,  running in the Command Line version of Maple is not attractive, as it takes away most of the interactive response with the program and produces results in linear form that are hard to read.
An old small 2 core PowerBook on which Snow Leopard runs is now our top machine, as long as the problem on the brand new machine is not resolved.
Do you have any further suggestion? We have wasted a lot of time and money on the new Power Mac so far.

Power Mac? Do you mean Mac Pro? Power Macs aren't capable of running anything higher than Mac OS X 10.5.8 Leopard because Snow Leopard and Lion are Intel-only.

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