As I've already stated - there is clearly a problem with the code, if the assignment files are not saving properly. It may be a problem that only manifests in certain conditions and with certain data, but it is still a code problem, none-the-less.
As there are unlikely to be any developers in the forums still using such an old version of Moodle, and as you seem reluctant to upgrade to a more recent version of Moodle (even within the 2.2 branch), you may well have to start digging through the code yourself to figure out what is going wrong.
You could try looking through the 'process_feedback' function and add the 'var_dump' function to output details of the variables being used, as well as using 'echo' statements to see which bits of code you are executing. Which version of the 'process_feedback' function you need to look at depends on what type of assignment you have created (offline, online, upload or uploadsingle).
If you can reproduce the problem away from the main site, with a copy of the data, then you might be able to set up xdebug + a suitable IDE and step through the code a line at a time to see where it is going wrong.
Aside from that, you may need to find/employ an experienced Moodle developer to track down this problem for you, with a copy of your live data - the list of Moodle Partners on moodle.com is a good starting point (including my own employers Synergy Learning).