In bitcoin world running a business for 6 years without a problem is unheard of.
I am not sure that PrimeDice site has never got troubles over its six year history, but even they got troubles, it does not matter because finally they came back, recovered, and grown well to become one of the biggest and most reliable, most favorite dice sites in online gambling. That tell us a lot of things about the Primedice's position in gambling world. I congratulate in advance for the coming six year anniversary of Prime Dice tommorrow, and I obviously wait for tommorrow post from @Stunna.
I dont remember any specific incidents where Prime Dice was in trouble, many trolls have tried accusing them of non payment but when put to test Prime Dice was always found to be legit. In these six years Prime Dice has updated their site too, and in few of the recent updates suggestions of players were also heard and implemented. Its also worth mentioning that in recent years Prime Dice has began to donate to charity, which I feel is a nice initiative by them.