There will always be a slight difference between the overall completion and file completion percentage, because the file completion only shows the percentage of blocks completed, whereas overall includes all data, including unchecked.
However as some people have been stating, in 0.5.9.2 and .3, deluge has not been completing blocks normally, resulting in this discrepancy increasing, but more importantly, leading to MAJOR loss of data on a recheck. It also makes seeding initially difficult, as you cannot seed until you complete at least one block.
I have rolled back to 0.5.9.1 and it does not seem to be a problem anymore. Additionally any data downloaded in 0.5.9.2 seems to be saved properly so I didn't lose too much data.
Someone here also said this was happening to them in 0.5.8.9? I don't know what that means, but if it's true it should probably be added to the bug report.
I made a post about it here: http://forum.deluge-torrent.org/viewtopic.php?f=7&t=7055
And there is a similar problem reported here: http://forum.deluge-torrent.org/viewtopic.php?f=7&t=7155
I have submitted a bug report here: http://dev.deluge-torrent.org/ticket/295
I would kind of appreciate it if we could get a dev response about this issue somewhere?