It's not a bug; ships have 1 AI ship class. It's not just used for determining what the ship does, but also for the build queue, so having multiple entries breaks stuff. Ideally, the devs should just set the colony ship AI to explore if no planet is available, like survey ships do when there's no anomalies. 

I look forward to reading the code. Maybe one day I'll actually play the damn game again... but for most of the previous week I've been sat watching endless soaks and praying the AI picks good techs ><

At some stage, you're probably gonna have to wade through the tech defs and adjust the weights; the basic ones don't make an awful lot of sense. For example, Institutional Research:

The high tech score makes sense... but I'm not sure where 20 military is supposed to be about. Compare with Zero Grav construction:

So... influence is 2 higher, wealth 2 lower, military 2 lower... yeah. Or the Harpoon missile:

Because, as we all know, missiles are all about making lots of money, right? Note that the military value of the tech is the same as it is on Institutional research. 

The thing is, if you look in the Drengin file, you see something rather different - the drengin weights on ZGC are:

Note the massively different scales involved in this weighting scheme. The Drengin have been more or less pointed directly at a few killer techs that they ought to acquire by around turn 100. Most of the others sort of putter about through tech; they've never got too small a chance to pick something, so they can pick more or less anything at any given time. They might choose a good one... but they might equally pick something completely inappropriate. This is basically how you have to code it if you only have a small number of scripts throughout the whole game, as 1 scripts has to cope with all situations across anything upto 100 turns. 

Having added so many scripts, each of which can alter the default tech choices differently, I can actually start to give the AI some tech strategies, teaching one to go for, say, engines early so their colony ships are better, while another builds up their planetary infrastructure so they can play a 'tall' strategy - and yet another can rush military tech and build an early military. But that did require going through every tech in every tech file to re-calibrate the weighting. I read about 150,000 lines of xml over the weekend... twice, so I could put them into a decent spreadsheet, play with the values, and then go back and change them all.

Any chance you can look at the Reapers (custom race) and see what they did right? The Reapers have consistently been at or near the top in my games.  As have the Collectors.