Just tested with a minimal set of mods:
- Project Cybersyn
- Cybersyn Combinator
- Ultracube
- Editor Extensions (for easier testing)
- (and any dependencies required)
The trains seem to behave as expected, speeding up immensely when the cube is in a cargo wagon.
Do you have a save file to test with? Also might be worth raising an issue on the Ultracube mod page, as they seem to have added specific compatibility code for this mod so they might have a better idea of what might be happening.