Does Caterpiller make 2 different 9 pin connectors?

It might, It really depends on how the adaptor for the scan tool you bought is setup to work. (knock of com 3 adaptor?) Best bet is to see if there is a cable available for your scan tool that is made for the truck standard 9pin.

The cat data link (CDL) adaptors have j1939(just on different pins) but doesn't have j1708, which the truck side will have, and with the year of your truck some of the computers may still communicate primarily over the j1708 side.
I've even seen early 2000's trucks that have the 9pin j1939 plug installed in them but don't actually have j1939 wired up at all, they just used j1708.