the file not found message is because of the way the gnutella protocol is designed (or atleast the way limewire and most other clients use it). each file is given an 'index number', and when someone searches on the network for a file, limewire returns the index number of the succesful match. however -- this index number can change over multiple limewire sessions, generally from adding or removing shared files. since limewire returns 'busy' instead of 'file not found' (if all upload slots are full, even if the file isn't found), other clients will continue trying to request the file that doesn't exist. however -- this should not effect the number of completed uploads.

the reason you're probably seeing less completed uploads is because of the new 'swarming' features that clients are adopting. only the newest limewire version (in cvs) displays the actual requested amount, counting the progress from there. prior versions would simply display the filesize of the requested file, and if the client requested the first 150kb of the file, the progress bar would stop at 1% and the status would be interupted (instead of complete). the newest version will correctly report the requested / completed statuses, so the overall completions will be higher.