The original pre-order of Combat Commander did include 2 bonus scenarios (#101 and #102) that were not included with the second printing. These bonus scenarios are now available for download from GMT's site.
As for the game itself, the only differences were
fixed German card #48 (called its order an action)
fixed pillbox count on American cheat card (information only, no impact on game play)
pinlines added to the hills on maps 11 & 12 for clarity
There were some cosmetic changes between the two printings. The maps are back-printed (meaning there is a map on the front and back of each mapsheet. The paired up maps are a little different:
First printing: 1/4 2/3 5/8 6/7 ....
Second printing 1/2 3/4 5/6 7/8 ....
Another cosmetic change...the counters on the first printing countersheet are only connected at the corners. The counters on the second edition of the second printing are also connected in the middle of each side. This results in a small tab that might be difficult to remove if you trim your counters.
But despite that long explanation - the changes in the second printing are minor indeed. I have the first printing and no one has ever noticed the small items that were changed (fixed) in the second printing. Both printings are eminently playable. And you will get the same stuff in both copies.