So it seems a mixture of doing the following:
-downloading and installing the ultimate version was a good start as I had way more issues with the other cd I had with the software on it
-running the program as an admin
-saving the files to a folder on the desktop instead of the default SS used, and setting it to auto delete the converted files after transfer finished.
as for the slow transfer, it was a bad disc, popped in a new one and it works wonderfully, transfers songs in a matter of seconds.
So for now I think it's good, I have transferred about 40 songs with no reboot.
Thanks so much!