When I want to split a line with Aegisub using the "split line at cursor", the end of the line goes on top of the beginning… Tried to find a solution on the net but haven't found anything…
It works the other way on my side. This is strange.
The only thing I can think of that you can do is as follows:
1. Go to View → Options → Hotkeys
2. Click "Subtitle Grid"
3. Click the "New" button
4. Create a new hotkey for the "grid/swap" command
5. Use this hotkey whenever you need to swap two lines (you need to select them on the grid first)
Hope this helps.