Hmm. Icy with geologicals should be industrial 2.4 + Extraction 1.8 as a baseline, I think - not a good starting point, of course!
Then the first refinery hub would be 1.2 and subsequent ones 0.8.
I'm surprised based on that you had most of those exports to start with at just two refinery hubs - but adding more should all else equal have made them more likely, not less. I wonder if the Wealth or Development Level boosts associated with the hubs happen to have favoured demand rather than supply for those items. There does seem to be some evidence that specialisation numbers are generated from system variables.
(Even at refinery 5.2 from six hubs almost all of those commodities are at best "possible export" on the theoretical model, many "possible import", so it's not entirely surprising that you don't have production of them, but it is weird that you had it and then lost it)
You are correct. Also, I was a bit mistaken regarding the sequence. Things were ok after 1st ref hub, then we completed 2 and 3 together, and messed up the market.
After consulting the game logs, the build sequence was:
29/4/2025 9:20 pm : Planetary Port, Economies: Colony 100%, only 4 commodities available
30/4/2025 10:16 pm : 1st refinery hub, the Planetary Port shows Refinery 240%
30/4/2025 7:34 pm, Economies: Industrial 240%, Refinery 200%, Extraction 180%
1/5/2025 3:18 pm Economies: Refinery 120%, Colony 50%, commodities present
1/5/2025 1:25 pm Economies: Refinery 240%, all commodities present --> this is strange, nothing was changed in system
1/5/2025 1:31 pm : 2nd refinery hub
1/5/2025 1:34 pm : 3rd refinery hub (we completed two at the same time)
1/5/2025 7:20 pm Economies: Refinery 120%, Colony 50%, commodities present
1/5/2025 8:05 pm Economies: Refinery 120%, Colony 50%, commodities missing ?!?!
2/5/2025 7:10 pm Economies: Refinery 360%, Industrial 240%, Extraction 180%
6/5/2025 8:29 pm : 4th refinery hub
6/5/2025 8:42 pm : Economies: Refinery 440%, Industrial 240%, Extraction 180%
7/5/2025 9:03 pm : 5th refinery hub
7/5/2025 9:15 pm : Economies: Refinery 520%, Industrial 240%, Extraction 180%
The 6th refinery hub was completed on 9/5, but economy still remains Refinery 520%, Industrial 240%, Extraction 180%, one day later.