Now this is a fairly new theory and I haven't yet had time to investigate it, but I will. I believe that I know why saidin is tainted. Everyone knows it was the Dark One's counter stroke at the sealing of the bore, but what exactly was this counter stroke? I think that he tapped his so called "true source" into saidin. This is what is causing Rand his channeling troubles. If you take a look at the end of CoS when Rand is helped by the mysterious man (almost certainly Moridin), when the balefire thrown by each of them collides, the result is what Rand seems to have been experiencing ever since then when he has drawn on saidin. Now assuming that this was Moridin (otherwise my theory is probably pretty off), he uses the true source, and as we have learned from Moghedien the true source has some serious set backs to its use, which sound to me quite similiar to the taint on saidin, but more extreme.