Given the rate of posts and their updates, I seriously doubt anything will come of this but hopefully someone else will read this and do something different.

So I just recently upgraded from Snow Leopard to Lion. Checked compatibility and everything seemed to be OK. In fact, after the upgrade, I was able to access the drive without issue (I use it to hold a VirtualBox VDI file that I want to access between a Windows machine and a Mac). I also created a single folder at the root of the drive.

Then I restarted the Mac and got an error from NTFS. I didn't pay much attention to the exception (and I should have, because debug logging was not enabled, if someone can suggest what other logs to query for this data I would appreciate it). But I noticed that the VDI file (60 GB file) was no longer listed in the drive's contents. It did show the space was consumed, however.

The folder I created was not touched.

So I followed the instructions in the FAQ to run chkdsk in a Windows environment. There was an error listed regarding the BITMAP attribute. But when the drive first mounted, I saw the file that was not displaying in OSX... then after a couple of minutes it was no longer accessible or showing up. But again, Windows showed that there was a portion of drive space that was consumed.

The folder I created was still intact.

Now, the first time I ran chkdsk I did not allow it to fix errors. So I re-ran it, and after it fixed it, the portion of the disk that held the VDI was wiped out.

The folder I created, wouldn't you know it, is still there.

I am in the process of recovering the data. But why would this happen in the first place?

Well, I was able to recover the data and I reformatted the drive (Tuxera NTFS), but VirtualBox thinks the file's corrupted. Fantastic. Use with caution on Lion I suppose.