Change client settings in DFGui only when client is stopped (be sure it is stopped by checking Task Manager), otherwise, even when you say "save config", nothing will be applied.
After you configure DFGui, start the client for 10-20s, then stop it again. Now check foldit.bat and try to see what settings are applied on line starting with ".\foldtrajlite -f protein -n native".
You could see something like this:
.\foldtrajlite -f protein -n native -qt -rt -i f -g 5 -p 10
Each corresponding setting (or switch, starting with "-") has the meaning described in readme.1st - I'll repeat it here:
When uploading only, the only switch used should be "-u t". Note the spaces - they are necessary for proper client functioning.Code:-qt use the quiet mode -rt use more memory -i f fold offline -g 5 update progress.txt every x structures (5 here, 0 denotes no progress.txt) -p 10 set priority of client to 10 (-20 to 20 are valid numbers)
DFGui does nothing else but applying those settings to foldit.bat when client starts.
The error you describe usually comes from the system that is not 100% stable (usually memory glitch) - no matter what all other benchmarks (including Prime95) may say - *.trj file gets corrupted while writing it to the disk. You can easily rectify it (if you were folding offline) by replacing "_42.trj" with "_41.trj" or even "_40.trj", and no work will be lost. In this case science scores will probably suffer a bit, as client has to redo wrong.
To avoid this error, back down your memory settings a bit, or your FSB. It will make the whole folding process more stable.
I've got to say that this latest client version seems to be more stable than previous ones (Linux and WinXP), be it while folding online, or no-net. Will take me another few days to check if the empty or corrupt filelist.txt problem has been rectified.