Guys a huge thank you!
I ponder the internal clock issue because on a reset the last time it knows about is the clock when alignment started, not the time when it was powered down - which implies the clock wasn't running, which would definetely contribute to the problems I encountered - and as my first alignment took 20 - 45 minutes would say why my GoTo errors were so large. By the end of the night alignment took < 20 minutes - so pointing accuracy on Jupiter was far better.
Alignment marks checked on both axis on each power down reset. Also checked vs the handcontrollers query - and the DEC alignment marks are spot on, but the RA is about 3 degrees out - the RA alignment marks should be a bit to the left of the marked position to get a 0 00' 00" reading so I countered for this later in the night.
Date wrong - well its MM/DD/YY so it wont accept 17 as a valid month, so I set 06/17/06 yesterday, only had a date error on my very first set-up.
Time zone is 10 for Sydney (and I pretty sure it was +10) checked this twice.
Time was entered both as pm but normally using 24 hour miltary time. I've been round the world 15 times now and can kinda do it in my head.
I used two compasses, both gave readings for 170 (I treat Celestial South in Sydney as 11 degrees East of magnetic South). I also roughly checked where the crux and two points intersect as a rough double check, and did a 20 mintue drift track on Jupiter and adjusted to improve. It wasn't perfect but it should be within 5 degrees.
Backyard has no concrete buildings or powerlines within 50 yards.
I thought modelling 3 points give you a complete sky picture - PLUS compensation for the drives not being properly polar aligned. I assumed the software was specifically looking to estimate and conteract this.
Mount stability - rock solid and not bumped all night.
Tripod base level - yes according to both my spirit levels and the internal bubble on the mount.
Scope as perfectly balanced as I could get it.
I have gone back to the Hand controller to drive it while its in the back patio.
No Polar alignment scope - probably the next thing I buy.
GPS - YES I think its my next major buy, from Andrews again if I can - that way its one supplier fixing all the issues and no finger pointing to somebody elses problem, and if doesn't work in the end its a warranty call.
Factory reset - very temped too.
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Questions on the GPS option. I presume it plugs into the hand controller, and is only present at the start-up time (otherwise you couldn't computer control the mount, unless the PC plug goes into the GPS? Or is it GPS or PC but not both in one viewing session?
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On the drive housings bumping. They are not round with a clear gap in all positions / rotations, they are horseshoe shaped and if you are looking close to SCP there are many positions which they will hit each other.
Similarily both the guidescope and the 90 degree diagonal can hit the tripod in the wrong positions looking near the SCP.
This is simply because the drives are too close to each other and the mount is not tall enough to rotate fully and not position the scope to collide with the mount or tripod.
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Well rather than viewing again tonight I'll likely just spend teh night websurfing trying to find a diagnostic or a fix.
Keep the advice comming guys - especially if you know of a suorce that has experienced and solved this problem.