Some adjustments to the loot system?

[Pells]

I think you're wrong on where the burden of proof would lie. Assume the one that actually makes sense over the one that doesn't unless there's clear proof to the contrary. And what proof does anyone have? That only a few people have noticed it happening? With 100 possibilities, there usually wouldn't be a tie anyway. (Ok, maybe a bit more often for 24 man content, but there how often do people actually check all 24 rolls for duplicates?)

Tie numbers, if possible, would be incredibly common. They would be roughly happening in a quarter to a third of four-man dungeons (assuming everybody rolls).

Math, for those who'd care:
Chance of no ties in four rolls for a single item: 99/99 * 98/99 * 97/99 * 96/99 = 94.05%
Six items per dungeon (two per boss): 94.05% ^ 6 = 69.21%.

This is for no ties, so the chance of seeing at least one tie in a single dungeon run would be a little over 30%.

With 8 people rolling: 99/99 * 98/99 * 97/99 * 96/99 * 95/99 * 94/99 * 93/99 * 92/99 = 74.8%.
You'd see it a quarter of the time in eight-man raids, as well.

A tie roll would practically be guaranteed in a 24-man run.