now what i sometimes or actually always do is time the universal translator perfectly so i get it right when secrets of creation and Alpha centauri are available so that once i get the translator i can pick up 4 techs at once(pretty cool eh?) the two free from the translator are secrets and then self aware machines and singularity mechanics from secrets. now the only problem with that is that it turns out that i only get 3 techs free. (it didn't give me sing mechs) and don't go telling me it's cuz someone else already got the secrets(they didn't) or because it's some twisted AI scheme to take over the world even though that's the most logical explanation.
Location: looking for a saviour in these dirty streets
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What you have to do is use the first free tech from the Unievrsal Translator to get an 'ordinary' tech. I've tried it myself, and you can't carry over the effects of a 'Secrets' tech. Use the first freebie to get Singularity Mechanics or whatever, then get the Secrets in succession (including Secrets of the Manifolds if you have SMAX - I once got all three in one go). Then you can use the final Secrets to get one more free tech.
Instead of problems with getting a tech, I've sometimes had the feeling that I've "lost" a tech. In other words, I got a tech in one of the usual ways, but later, when I thought to use it, it seemed like it had disappeared. I don't recall a clear example of this (aside form never being able to build Temples of Planet in my original SMAC v1, which seemed to be a version problem) because I've gotten distracted by other events (you are generally in the middle of something else when techs arrive) and didn't try to utilize the tech right away (except for the T of P thing).
I've since figured out that you can't build a Hologram Theater without a Rec Commons (at least in my SMAC v4) despite never seeing any documentation to that effect, so some of those times were probably when I got the Planetary Networks before Social Psych and found that I couldn't build a HoloT after all. There may well be other techs whose fruits are dependent upon additional stealth-documented prereqs and so may seem not to be there unless you look at the (F2) tech detail instead of just what you can build.
I also have the feeling that the AI has sold/traded to me, or at least offered to sell/trade, the same tech I only recently got from them. Sometimes I don't pay too close attention to a string of trades, so I'm never quite sure about this either.
{Aside: Bogus trades would be an interesting addition to MP; where you could promise a tech you didn't have or just stiff the other player and not deliver, or sell them the Brooklyn Bridge (on sale today only!!).}