You probably have a mod enabled. That's exactly what I got when I had The Mars Effect enabled, as soon as I disabled it everything was fine again.

either fleet size is bugged or its only the display being bugged, havent actually gotten to ~2000 supply to check.

You should start with more than 100 FPs if you turn it up to Large, no?

Same here, fleet size starting option has no effect.

Here's how it works.

From the gameplay.constants:

fleetSupplyData-Small
fleetSupplyScalar 0.75
fleetSupplyData-Normal
fleetSupplyScalar 1.0
fleetSupplyData-Large
fleetSupplyScalar 1.25

Basically, at small you get 75%, normal is 100% (default), and large is 125%.

The default start is 100. If you start with Large, you'll get 125. Works so far! Now take the first research. It moves you from 100 to 250 (so it adds 150). Do the research at Large, and you get 312 as the new max instead of 250. 25% of 150 is 37.5, in addition to the initial 25 = 67.5 "extra". 250 + 67.5 = 312 (game always rounds down).

The short version: whenever you gain FPs, the setting modifies how much you gain

Yeah, the actual numbers on the research are static, but the increase itself does work. The numbers are read from the actual research files, and displayed "stock" before any modifiers are applied it looks like..