Did it ever work?

Not a plumber, but I'm going with... Your return valve is set improperly, or one of your booster pumps isn't kicking on... or both things aren't working. The two jets that are working are probably the same jets that work off of the filter pump.

I bet your pool builder could solve this in a couple of minutes.

No it never worked right. Not sure what you mean by my return valve? All the pumps are operating normally when I turn them on and off. The contractor said that he plumbed 5 of the jets to be on the 2hp Whisperflo pump and that they went directly to the jets and the other 5 along with circulation on a separate line on one of the Intelliflow 3 hp pumps. The only 2 good jets that I have are both off of the 2 hp Whisperflo that goes direct to jets and not through the filter and heater like the other ones. That being said, I still only have 2 off of that particular group of 5 that are working properly. I am extremely frustrated and confused and not sure where to go next with things? Thanks for your help

Is there any automation involved?

Please post some pics. Put the pix in a photobucket album. Copy/paste the 3rd option to the reply box, one pic per line please.

If you have pics from the construction at different stages, specifically, just before the shell was shot and the equipment pad, they would be the most help.

Scott

there is a good chance that you have WaterWay jets, which have an adjustment to slow down or stop waterflow. We always remove these internal stops to prevent the problem you are having. The face of the jet turns to stop or start flow.
A picture would tell for sure.

It is also very possible that you have reversed one of the water / air connections which can have strange results ranging from only a few jets working all the way to water shooting out the air vent. More info on the make of the jets will likely yield a definitive answer.