The first time, they had shields and we didn't, and they had a capship that was actually invulnerable to everything.
The second time, they unveiled WTFPWN beams and Juggernauts, and still only got as far as Capella.
In the alternate universe, a pair of destroyers, a trio of corvettes, and a few cruisers and support ships ate a Juggernaut, a Lucifer, and eight or nine destroyers for breakfast. Granted, the Lucifer got taken with help, but the Juggernaut and four destroyers went down hard and fast, without Vishnan help, and without friendly capship losses. In a situation where resupply was difficult, repairs were done quickly, with minimal outside support, and there was no loss replacement.
With full logistical support, loss replacement for any ambushes or a few stupid mistakes, and the might of the full Terran and Vasudan armadas, the Shivans are hardly likely to "om nom nom" anything but beams.
Yeah, the GTVA can't straight up WIN against the Shivans, mostly because we have no knowledge of their full strength, the location of any production facilities, or anything of the sort, they can sure as hell make the Shivans lose too.