I'm using the latest version of Backwpup, and really think it's a very good plugin. I use it on numereous site.
With the latest version I noticed that the backup is made (sql=56Mb), zipped (5,4Mb) and mailed to me with no problems, but the window keeps hanging around 41 to 71 percent. So I didn't know if the table checks and optimisation occurs after sending the backup. Looking at the log it showed that the weren't.
So I split the two tasks: one for the backup and the second for the checking and optimisation. Both work fine en the logs show the job ended in .. seconds. But the window that shows the progress always hangs somewhere.