Either I'm missing something, or KER doesn't currently understand decouplers correctly. Observe these three images. In the first I have a heavy craft consisting of a science lab, a probe core, a fuel tank, and an engine. Its mass is 4203 kg, and it gets only 435 m/s delta-V. In the second image I've separated the heavy science lab from the rest of the craft with a decoupler. Note that the decoupler is staged after the engine, so the delta-V should not have changed significantly (the decoupler's mass is tiny). However, KER now thinks it gets no delta-V at all until the science lab is decoupled, after which it will get a whopping 4271 m/s. So it's more or less as if the science lab had not been attached in the first place, as in the third image.