I imagine it's to do with the debacle over our financial irregularities after we beat Sunderland in the Play Off final in 1990. We were demoted two divisions (which would've meant Tranmere were promoted to the 2nd division), but was changed to demotion one division meaning the Trannies didn't get promotion after all.
I thought it was the floodlights in '93. Probably both.
They definitely do hate us though. Some pikey twat shouted "what goes round comes round cheating Swindon cunt" (or words to that effect) at me as I was walking towards the ground before the last game of the relegation season a couple of years ago. I was genuinely bemused by that for ages