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Hey Eric- visits are always counted no matter where it falls on a visitor's path. If your PPC channel manager (such as AdWords) shows 100 visits, Omniture should also show 100 visits. If these visit counts are different, signs point to a problem with your appended tagging or your rules for identifying those channels (such as the s_cid could be falling off in the URL parameters).

The concept of credit only pertains to the conversion (orders, revenue), so you will definitely see a discrepancy between your PPC channel manager and Omniture last click credit since your PPC channel manager does not "know" the true last click of a user like Omniture does.

Hope that helps.