The missing file extension is a known issue, one that we've already filed with the dev team to resolve. I believe we've also opened a bug for the missing data, if you haven't already opened a case with the support team your data might be useful in figuring out that issue.
Yep. A couple weeks back I uploaded all the log data. They were not aware of this issue at the time. They did manage to replicate the bug, and are working on a fix now....
Latest response from support as of today (I have not had time to do this):
I have been working with development and I haven't seen any resolution for this issue from them yet. However, if you are willing to try something that seemed to work for me on your configuration. Turn off your remote access control. Part of the testing that the development wanted to do was see if the issue could be reproduced on a remote host. I found that you had remote access control on. I turned it off to do my testing and the issue resolved itself. The file extensions were still missing, but the data was in the files. The file extensions issue has been resolved in another bug, I'm just waiting on a hot fix release for that. This would just be a testing scenario to see if turning off remote access control also fixes the issue for you or if it was a fluke on my end. Please turn it back on after you have confirmed or denied this.