The readiness monitors also have to be set. This is to prevent you from just clearing any CEL's you might have in the parking lot of the emmissions place and then passing the test. there are 7 - 10 readiness monitors that report on a many diferent systems in the engine and emissions system. The monitors typically take five or more drive cycles.
Anyway, if you are clearing a CAT related CEL ocassionally, or using anythong other than an AP to mask the code, I would be very carefull about getting the emissions checked and only do it after you can verify that there are no stored CEL's and the readiness monitors are set. You can check the readiness monitors with a good CEL reader like the ones they have at most Autozone type places. That is what I did and it worked like a charm (no cat at all on my 8).
Not sure my explanation is as clear as it could be, but this is the best I could explain it. Ask if you have any questions.