Well, after an hour of searching through old threads, i came up with a couple of conclusions.
1. the freq cycle time of the new keyless entry might not gel with the other remotes, meaning that they can't be used at the same time.
2. It may be as simple as the order in which these things are programed
3. it may be the logic board. (i dont think this is the answer because everything else works.
What will i attempt. Well, I am down to clearing all the codes and trying to re program in a different order, (ie one hand held remote, then the homekey or whatever the little buttons built into the wifes car are called and then the keyless entry. If i can get those to work, then i will try the last hand held remote.) Apparently this might work.
The wife is nervous that if i clear the codes, that the keyless wont work anymore and she wants that for our son in case he forgets his key and needs in. Maybe i will wait till spring. seems silly for her to have to get out of her car, punch in the code, drive into the garage and then shut it via the wall mounted control, but whatever floats the boat. saves me some frustration in the mean time.