Couple of things.
1) Maintenance. Your buildings that you're using to produce your hypothetical 100 production and/or research have maintenance, which is counted in your spending. Therefore, you'll never be at 100 anyway.
2) Build queues. If you're not building anything in your starport for that planet, the money that would be spent on military is returned to your treasury...and isn't actually spent. Also, social gets a larger piece of the pie, although the math escapes me at the moment (it's 4am here) for exactly when and how and why military and social get their piece of the pie, and exactly how large it is. This also works in reverse, except that unused social is diverted to military before it itself is returned to the treasury (though it's only the base value, which makes me question the 1/99 strategy a number of people here use).
Suffice it to say, if you want a ship built faster, stop building social improvements, and by the same token, if you want that factory to build faster, stop building that ship. This is of course assuming you aren't running at 100% in the given category to begin with.
3) Rounding. I've noticed lately that there are slight "rounding errors" within the game. While rounding can and does happen, and one would expect, say, 25.6 to be rounded down to 25 (and as such due to rounding and percentage spending you could wind up with a net difference of a bc or two in each direction...possibly per category, but I'm too tired to figure that one out). However, I've been seeing, for instance, 25.0 get rounded down to 24.9 and then get rounded down to 24. I'm not entirely sure what causes this, but it's annoying. I posted a bug report on it, and verified the problem exists in TA as well, but apparently no one else is bothered by it. 25.1, however, is rounded down properly to 25, rather than 24.
4) Output. (This is the big one.) You're only going to spend 100BC/turn on research if you have (total output of research buildings) * funding equalling 100. This is discounting focus for the moment as that tends to complicate things, but if you count production rather than base then you can account for it, and that's probably a better way to do things as then you don't have to multiply in production bonuses (rings, planetary improvements tech, nano recorders, hyper computers, production modules on economy starbases). If you have 120RP capacity and you set it to 100%, you're spending 120 on research. Alternatively, if you only have 60MP capacity and you set THAT to 100% (let's assume this is one planet, for simplicity's sake), then, assuming you're building something on that planet, be it a ship or a building, you're spending 60BC.
I hope some of that makes sense.