What platform are you playing it on? If it's a Xbox or PS3 have you checked for updates/patches for the game? I know that one exists for both the PS3 and Xbox.
Another question if you are on console, is your hard drive full? A full hard drive can also cause games to not save properly, this applies to all games and not just borderlands.
Sadly to address your lost items issue, as with many things in the digital world. When a file is saved with certain information, that's the only information that it has to access when the file is reloaded. So it is highly doubtful that you will get your items back. You'll simply have to replay that part of the game and hopefully get the same quality of item (I assume your loaded save is before the point in the game where you got your stuff).
Another possibility is that you weren't logged into your account, but under someone else's? I had that problem when roommates and I shared a PS3 and Xbox.