Good stuff, Mal!
It's very easy for things to get so out of whack! I still think your initial problem came from a secondary that wasn't square to the focuser - if the secondary wasn't centered but still square to the focuser, it is still possible to achieve a properly collimated situation. What not centering the secondary does is not maximize the amount of light going into the eyepiece. Not having the secondary square is the source of your collimation troubles.
So, by taking time to centre the secondary, you also set it square to the focuser, and everything fell into place! How about that!
Bojan mentions off-setting the secondary. If you are doing photography, this is
more important than for visual. The percentage gain for visual isn't all that significant, and for most observers more of a pain in the bum than a help. Photo is much less forgiving, especially with fast f/ratio Newts! If you really want to off-set your secondary, the minimum you should do is set it back from the focuser anywhere between 1.5mm and 3mm depending on the size of your Newt. The other axis that can be off-set is the long axis, and the sec lowered towards the primary again between 1.5mm and 3mm, depending on your Newt. There are various formulae provided on the Net for the exact amounts for your Newt, just do a search for
"Newtonian secondary mirror offset"
On my big 17.5" dob, I put a little permanent marker dot on the secondary, along the long-axis where the off-set will leave the laser pointing at, which is a little higher above the sec's centre. However, I don't bother too much about it. I leave the secondary centred in the Cheshire. BUT, I do have the secondary set back from the focuser by 3mm. It does alter a little the co-centricity of the reflections that are seen, but that's not a problem for me.
My big dob is my only Newt I bother to have off-set the secondary.
If you do intend to do astrophotography with your Newt,
DO look into offsetting your secondary as Bojan mentions.
Alex.