So while the GTVA might know a lot about a Shivan fighter's targeting array, it's far from sure that the big ships would use the same stuff for their weapons.
Why would they use a different sort of sensor at the capital ship level? Unless you can answer that question coherently (and I doubt you can, short of conspiracy theory that the Shivans anticipated their craft being captured and ignored the logistics advantages of uniform systems), the bottom line is that the GTVA still knows enough to white-noise the hell out of them.
I never said anything about a different base technology, but obviously a capship packs more and much bigger sensors than a fighter. Since it would be odd to build something far bigger than necessary, it's only logical to assume that capship sensors are bigger, because they pack additional features and power.
The additional power alone makes them harder to jam and the additional features might include ECCM equipment, wider range of frequencies and who knows what else.
And just being able to detect a sensor sweep that is directed directly at you, doesn't mean you are automatically able to jam it.
Beside that, the Shivans have shown to be very adaptable. Even if the GTVA or UEF would succeed in jamming a Shivan ship in any way, I wouldn't expect it to last long (neither in the actual engagement, nor in the war).
All that combined means there are plenty of non-conspiracy reasons to justify why GTVA and UEF ships can't jam Shivan capital ships (or be less effective at it than against other Human ships) if the storywriters want to have it that way.