Can't Seem to Get Clean Up Threat to Work

It sounds like you've got some large archives with many files in them stored on your computer.  When doing an on-demand scan, all archives are expanded and their contents are scanned... eating up large amounts of drive space temporarily.  You can see if this is your problem by temporarily disabling "scan inside archives and compressed files".  This will most likely resolve both your issues, but may also not cause any detections.

In the quarantine manager, do you have file paths listed for the detections that have already been found?

Thanks for your reply, Andrew. To answer your last question, yes, Quarentine Manager does provide file paths for the detections it has already found (five that it says it can fix, one that it says must be cleaned up manually). I haven't had a chance to play with this for a day or two but I just initiated another clean-up of one of the detections that the software says it can fix so we'll see what happens.

I did as you suggested and removed the check from the box that says Scan Inside Archives and Compressed Files, but when I initiated a scan of local drives, it still says it's going to analyze over 7.2 million files so that didn't appear to change anything. It seems to count fairly quickly but at the rate its counting it will take a long time to look at all the files. And I really don't want to limit the number of files it looks at because, as you said, that might speed up the process at the expense of leaving some bad stuff on my computer. 

The system still says it's trying to clean-up that file but there's really no way for me to know if it's still working or just sti\uck in some kind of loop. I'll provide another update after the software has run for a while and we see what happens with this scan of local drives I just started.

Didn't accomplish much. When I left the house late yesterday I let the scan continue to run - it had counted down to abou 6.4 million files left to check - but when I got home several hours later it was no longer running, there were no error messages displaying and the Quarentine Manager - which had some items in it when I left - was empty. When I open up Scan Local Drives now it says the scan has never been completed and it indicates no threats detected. Very frustrating. Any suggestion on what else to try? If not, I think I'll remove the software and move on to something I might have to pay for but that is a bit more reliable.

The only other thing to try is disconnecting all external storage devices and disabling Live Protection.  If there's still a problem, we'll need to get the product team's attention, and send in an SDU package (generated using the SDU tool discussed and linked to here: http://www.sophos.com/en-us/support/knowledgebase/33556.aspx ).

Clean up takes forever ie 8 hours and you cant shut it off or shutdown your machine plus you dont know if the clean up is working - really frustrating

Clean up definitely shouldn't take that long... a standard cleanup takes 10 minutes, max (usually more like 30 seconds).

What detection are you trying to clean?