I ran across this each time I use the "Move selected line" shortcut (which is a very handy feature), after I use it and don't follow up with anything else (such as entering a new line or other text modifications) when I leave that note and come back the line I just moved will have moved back to were it was. Funny, for a while before I discovered that this was a bug I thought I had forgotten to move the line, moved it again each time and thought my short term memory was failing
I then tried moving several lines around instead of just one, as long as there isn't a text modification such a carriage return, everything will revert back if the page is left and subsequently returned to. When you are able, please look at this.
Thank you for your patience guys. Indeed, it was a bug. Fixed! The fix will be available in version 2.68 and 3.04 beta.
The reason why it was happening is banal - this kind of text modification wan't makring text as modified, and, therefore, changes wasn't saved. Here is a temporary solution how to go around this issue - simply modify something it to the text. For example, insert a char and delete it at once.
P.S. Please sorry for taking it so long to respond/fix this issue - so happened that somehow I've managed to mark it as "read" (resolved).