Rohan,
My LX seemed to do the same wierd thing (on Auto Align) as yours tonight so I spent some time trying to diagnose the problem with auto alignment.
Every time I have used the LX so far it has been around 8-9pm and the alignment and goto have worked perfectly. Tonight it was after midnight. The first two nights at 8-9pm the LX was pointing very close to the alignment stars (Sirius and Canopus) but tonight the LX was 90 degrees (az) out with Canopus, the first star selected for auto align. Once I worked out where Canopus was and pointed to it the LX then pointed to the second alignment star (Rigel Kent) reasonably accurately. Once alinged with Rigel Kent the goto was spot on with Jupiter appearing in the centre of the crosshairs on the finder. Are you 100% sure that you are correctly identifying the alignment stars. Rigel kent is a good choice because it's a bright double and almost impossible to mis-identify. My initial guess is that it may be a software bug with the LX incorrectly slewing to the first alignment star. I will try again at various times both before and after midnight and see if I can track down the problem as I suspect it may be time related. I still haven't trained the drive but I have corrected the Lat/Long with figures from my GPS. Unfortunately in the hour it took to work out what was going on the dew beat me, but not before I had checked out a few favourites. Hope this helps, I will check further the next clear night.