Problem lauching Transceiver Toolkit

I am having the same issue with Quartus 13.0sp1. System Console works correctly but Transceiver Toolkit does not: I get the error ": "Please put Quartus in your path and restart System Console before attempting to use Transceiver Toolkit". I do not see where this path is set. One clue may be that the directory in which my scripts are stored (and shows up in System Console) is not the default system Console directory under the installation directory. I think this may have been changed by a co-worker, but I do not see where this can be changed. I have tried uninstalling and re-installing Quartus, but this doe not fix the issue. Any help would be much appreciated.