What MoBo are you using & what OS. I would be intrested in comparing your processing time to mine.
I'm running an XP 1600 w/512Mb. under Red Hat Linux 7.2 (Cannt remember the Mobo at the moment)
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There is a Linux version, but it is slower than the Windows version. Depending on the setup, some have gotten best results by running the Windows version in WINE in Linux. 
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I am running SetiAtHome under WINE as well & find it to be about 15 to 20% faster.
I figured out how to set it up to run under Wine and send to my SetiQ proxy :
wine -version nt2k -- <name of seti exacutable> -proxy <your proxy settings>
note the double "-" between the wine command and the program to run. This allows you to send command line arguments to the program to run under wine.
Also you are using the windows executable not the linux one.
I set it up in a shell script to make it easier to run.
Also make sure you use the Command Line version rather than the GUI definetly faster.
Oh & Welcome to the team!!!!!
Alric