I'm not 100% sure, but I believe the bug report is correct that it was broken in 3.9. I remember the initial USB support (3.7 I think) had a lot trouble connecting, but once connected it was pretty stable. Then it seemed like the connection problems improved, but the transfer became unstable. I think that happened in the original 3.9 release. Strangely, I don't think anything was mentioned in the release notes about anything being fixed or changed regarding USB, but I'm pretty sure that's when it happened.
Sorry I can't be more specific. I could maybe try downgrading to 3.8.1 and see if the transfer is more stable in that version if you think it would help. I have no idea what the code looks like, so it may not be realistic, but maybe you could look at a diff of the relevant code in 3.8.1 and 3.9 and see if there were changes in any suspect areas?