I've relized that 1.4 is out and upgraded from 1.3 and the problem is now gone.
The problem was that my system drive is E: not C: and I was getting a disk not in drive error around 127/31280 and for other patterns onwards.
I was going to check and suggest that it lookup the %SYSTEM% path from windows and then use the drive letter from this as the system drive to scan.
Also that the "Cancel" button does not do what I'd expect, to cancel the Scan, it seems to do the same as the Continue function, ignore this problem and carry on scanning. This is during the Could not access /Disk/Harddisk2/DR2 with Cancel, Retry, Continue.