I have a compare job run for 46 hours and only 14% completion. Is it normal?

If the table is large and there are a number of rows out of sync, compare or repair could take some time.  I'd recommend you open a Support case.

If this is a production issue, you can call support at 800 306 9329 or 949 757 8000.   For less critical systems, you can open a case online http://support.quest.com