If you just got the CableCARDs installed today and repeated Guided Setup, it's possible the box is still indexing all the Guide data and that's affecting performance. Give it a few more hours and see if the problem persists.
So is it an S3 or a THD? Your thread title says Tivo HD but you say S3 in your post.
So is it an S3 or a THD? Your thread title says Tivo HD but you say S3 in your post.