Question about research...

[WoodMan]

I don't think your missing much, it sounds to me like the reason the Actual Outputs are not going higher is because you have already reached the Total Empire Potential like you mentioned.  The reason you have slightly more than your Total Empire Potential I have to admit I don't know, but my guess is its something to do with some bonus from a ruin or something.

[Aures]

A racial or government research bonus is applied to your total Empire potential. Try starting as a technocracy and then immediately have a revolution to see this effect. The racial bonus can be demonstrated to work in the same way, but it is slightly harder to make a good comparison because of the non-linear way the total empire potential grows with population.

A ruin research bonus is completely different. It affects the calculation that turns your Maximum Potential into your Actual Output. Here is a table I just made for one of my games (Sorry about the full stops, this BB ignores more than one space in a row and tab characters. Let me know if it is misaligned or hard to read for you):

Energy.......HighTech....Industrial...Weapons
1488..........1584..........1224..........1344..........measured Maximum Potential
1488..........1584..........1224..........1344..........calculated Maximum Potential
693............369............570............313............measured Actual Output
693.3447...369.0383...570.3319...313.1234...calculated Actual Output

1314..........measured Total Empire Potential
1945..........measured Total Actual Output
1945.838...calculated Total Actual Output

The measured Maximum Potential, measured Actual Output and measured Total Empire Potential are the appropriate values read directly off my research screen. The calculated Maximum Potential is what I get when I add up all of the values in all of my individual research stations, included to demonstrate it is the same as the measured Maximum Potential. The calculated Actual Output is what I get when I run the Maximum Potential through the formula I discuss later. The measured Total Actual Output is what I get when I add up all the values in the measured Actual Output. The calculated Total Actual Output is what I get when I add up all the values in the calculated Actual Output.

The formula I use to turn the Maximum Potential into the Actual Output for each category is:
Actual Output= Maximum Potential * bonus factor / measured Total Actual Output

Where the bonus factor is 1 if you do not have the planet with the appropriate research bonus ruin and 2 if you do. I have the Akurian Industrial Workshop (empire wide 100% industrial research bonus) and the Energy Engineering Facility (empire wide 100% energy research bonus) so my bonus factor is 2 for Industrial/Energy and 1 for HighTech/Weapons. As you can see the numbers work out as close as can be expected, there are probably other circumstances where rounding means the numbers might be off by a k or two.

BK6583, if you run your numbers through the above formula you should find that solves the discrepancy.

If you get all of the research bonus ruins your Actual Output will be doubled. Considering you have to more than double your population to double your stated Total Empire Potential (at least in big empires) and build the research facilities to actually do the research, colonising planets with research bonus ruins looks like a good idea in most circumstances.