At first I thought this was a bug related only to the neutrality learning center, and caused by the fact that you have two tech branches both leading to similar buildings. But yesturday I conqured some enemy planets and aquired new building tech, specifically virtual reality modules, and ended up with multiple structures from that tech tree on my to build list. That is, I could build both entertainment networks AND VR centers? (don't remember their exact name, the +morale structure, not the trade good!) on my planets. This underlines a bigger problem with the engine then I thought.
Basically it will only properly replace the "current tech" structure if the higher tech structures are discovered in an exact specific order (the order in which they would normally be researched). Any diviation from that order results in breakage of the autoupgrade and the colonial building engines...
So any time that you:
1. Research Neutrality learning center out of order. - Tested
2. Capture tech by conquering a planet out of order. - Tested
3. Trade for techolongy w/ alien races out of order. - Assumed... can someone verify?
There is a good chance that you end up with multiple structures of the same type from different tech levels on your planets construction list, and that they would not upgrade properly...
Also, I am pretty sure AI surrendering to you adversy affects the whole system aswell.. I think their planets don't autoupgrade when that happens or some such... (or maybe they didn't use to, I don't remember anymore).
If this bug is solved, it will take a while. So can anyone share a workaround? specifically, a method to "call" on whatever function it is that autoupgrades planets and cleans up the "build interface" of colonies that I could use in the meantime?
USERS: DO NOT UNDER ANY CIRCUMSTANCE POST A RETARDED AND USELESS COMMENT SAYING SOMETHING TO THE EXTENT OF "Well, duh, then don't get tech out of order, bug solved". The developers don't need you to "protect them" from bug reports, this is not working as intended which makes it a BUG not a FEATURE. I don't care how hard you the user thinks it is to fix, if the developers decide so they will tell us it is a bug they cannot fix at the moment. It is sad that I even need to post this note but experience tought me otherwise...