Delete E:\SAVES\PCSXBOX\pcsx.ini via FTP or using the file explorer/equivalent of UnleashX/XBMC/DVD2XBOX/etc
If you want to keep the memory cards/save states/etc for games you've already run, but want to reset the configuration for them, you have to just delete the [GAMENAME].KEY and [GAMENAME].STG files in each E:\SAVES\PCSXBOX\[GAMENAME]\ directory.
Or, if you want a totally clean start and don't care about any PSX game you've run before, you can just delete the entire E:\SAVES\PCSXBOX\ directory.