Actually, the transport has sensor-proof armor, not some kind of jammer.
And, as for the thing, the point of confusion is that the target is unable to tell what is an enemy and what is an ally. Also, if this helps, the spell that did it was a scrambler, and that means the Interceptor II's computer systems would be on the fritz (anything system that is linked to the computers would be haphazardly switching on and off or randomly firing), not that is would be enraged.

Niz manages to get the transport's systems back online!
A portal appears in front of the transport, and the transport goes in, with the portal dissappearing behind it! The transport has excaped via jump drive!

Note- the grappling hook is unfortinatly still there and has kept part of the portal open. The remaining part of the portal is too small for anything to move through or the grappling hook line to properly move through, so now the line is stuck there. So, therefore, the Interceptor II and the transport are both immobile. And the transport did not jump drive to the Warp Gate. It jump drived in the opposite direction.