I recently bought a 6SE myself, and had some similar alignment problems initially, in addition to "runaway slew" problems where the scope would start moving uncontrollably past the object selected, and I'd have to hit one of the movement arrows to stop it.
It turns out that if you surf around on the web, and look at the Celestron FAQ for the 6SE, that the scope is very picky about having enough power (current and voltage). It malfunctions in strange ways if there is insufficient power.
I was using very good Energizer rechargeable batteries, but it turns out that rechargables only provide 1.2 to 1.3V and the Celestron really really wants a solid 1.5V (per battery), or 12V (all 8 batteries).
So, make sure you have good power if you have any positioning problems.
There are two alternatives:
1. Use high quality alkalines or long life Lithium (not Lithium-ION rechargeables!)
2. Use an external power source (needs a separate thread I think because there are so many options).
I ended up buying a JumpStart unit from Super Cheap auto and virtually ALL of my alignment problems have disappeared. The scope moves with confidence, and the JumpStart unit has powered my 6SE for 8 full continuous hours many times and still had plenty of power left (plus I had my iPad plugged into it as well). While at first it seems these units would be a ridiculously risky low-quality option (they are <$90!)... I am an electronics engineer and disassembled one, and essentially you are getting significantly cleaner more stable power from one of these cheap units than you would your car battery. There are downsides, as you need to keep them "nearly charged" most of the time. Letting them run low can shorten their life. But, considering that 8 Lithium Energizer AA batteries cost $40 alone, The SCA jumpstarter is actually a great value. If you want more reliability, just buy two!
Interestingly, the little cable inside the jumpstarter box will fit the Celstron perfectly, you don't even need to buy any cables! You can also get a cheap 12V extension cable at any SCA store for $12.
If you do use an external power source, be attentive to the power cord and make sure you either turn the Cordwrap feature on, or be very observant to be sure the cord does not wrap around the unit during positioning.
(Here is a link to a page containing the units I described:
http://www.supercheapauto.com.au/onl....aspx?id=70601)