Display MoreTime for creating 25 UU-matter with scrap, and scrap count:
512 EU 405 sec 840 scraps
1024 EU 202 sec 841 scraps
2048 EU 100 sec 845 scraps
4096 EU 61 sec 810 scraps
8192 EU 37 sec 760 scraps
16384 EU 30 sec 612 scraps
So as you can see, without scraps it's linear, but with scraps, something happens around 3k EU.
(in the test the scrap flow was constant, even with 16kEU the scraps never went below 30-40 in the massfab gui)
Probably what happens is that on one tick, you get 5000 (or so?) EU worth of acceleration from scrap. If it gets 3kEU, 3k of that is used up, and there's only 2k left on the next tick, so 1k of the 3kEU/t doesn't benefit from scrap on that tick. The more energy you give it at once, the worse this gets.
If you have enough scrap to keep up with that kind of energy input, it looks like it's better to add more MFs than to shove more than 2kEU/t at one...