[Jessica_L]

If you're not quantitating via qPCR, you run the risk of this issue as discussed above:

(3)One big problem with fluorimetry over qPCR is that intact amplicons look no different than non-intact amplicons. So if your library is only 10% full amplicons through a failure in ligation, etc. then qPCR will tell you that. But fluorimetry will not.

It's hard to say definitively that this is why your cluster densities are low, but if the problem is not with the library prep kits or with your MiSeq reagents, then library quantitation is worth looking at. I understand that you've not had problems with other libraries, but maybe there's something about the Sureselect method that causes it to be less efficient. qPCR would tell you for sure one way or the other if that was your problem.