There might be a improper link between an earlier tech and a later one that is letting you skip over the marked techs. I'll take a look.
No, I didn't skip over intermediate technology. I researched the intermediate technology (the middle red arrow in this case), got the planet, researched later technologies, and then at some later point that "get another planet" technology became available for researching again.
It wasn't the only case in that game, either. Do you see that magnifying glass in the third column? "Get an extra slot on a planet"? In-between Mental Scheduling and Genetic Labs? I researched that twice in total. That is, I researched it once, then researched later technologies, and then the magnifying glass became available again, so I researched it a second time.