6 gearbox question

[mackat]

Took the gearbox off to transfer onto my other engine and in the process thought I'd clean it up a little.
In doing so I undid all the bolts holding the 3 sections together.

Cleaned it up, painted it - all good.. but when I start to tighten down the bolts it goes into gear and I can't get it out.

With the bolts loose, I can move it in/out of gear.

I'm I doing something wrong?
Also at which position is natural?

Thanks