no
the only purpose for the auxillary system is to operate the boom if the main power source goes dead, it is a safety system put in place to get you down to the ground in a case like that. The auxillary motors run on their own circuit.
But that is interesting that the boom works in that circuit and not in the normal one.
Now i know this let me check a couple more things and i'll get back to you if i find something.

Well i have found that the secondary boom lift will work if you use the auxiliary pump switch. shouldn't the aux pump come on with the primary when trying to raise the secondary boom?

yes that is my understanding also.

just to clarify your interpretation of which boom is primary and which is secondary
- primary boom is main horizontal boom arm with extension cylinder that platform is connected to
- secondary boom is the main boom sections (the Z section that is for vertical elevation).

although you have changed the primary and secondary porportional valves with no change in operation i just need to clarify this so i can check a couple more things out as possibilities.

the full model and SN are :
Z30/20N RJ
Z30N14-15407
As you suggested I tried swapping the primary and secondary directional control valves and the problem stayed. I also tried swapping the relief valves and still no change. Also yes the problem is the same at the platform and ground controls.

does this happen using platform and ground controls?
then yes i would look at the main manifold valves.
what is the full model and serial number of this unit off of the name plate located inside the tractor unit on the panel beside where the boom arms are.

Well i repacked the cylinder and i am still having the same problem. Could the cylinder valve block be the trouble?

I checked pressure on each line coming out of the manifold and have 1600-1400 PSI going to the secondary cylinder. So eyther the seal is bad on the piston and there is an issue in the valving on the bottom of the cylinder. Does this sound right?

brewski is on track here
get a test guage (5000psi) and put it in the test port on the function manifold. The test port has a quick disconnect fitting with a rubber cover on it, you will need to get the opposing (female) quick disconnect of the correct size to plug onto this. Or you can just remove that and tap straight into the threaded port , either way works.
Verify that you are getting pressure when activating that function.

system relief pressure should be around 2800 psi
primary boom down 1400 psi
secondary boom down 1600 psi
(these figures are based on a specific serial number range and may not apply to your unit, you will have to look up the manual for your specific serial number range on the genie website in the service manuals section).

Verify the problem is consistent between the platform controls and the ground controls to help isolate where the problem is.
If it does the same from both control panels then your problem is in the function manifold valves. Since you've replaced the counter balance valves on the cylinder i presume you still have to locate and check the 'check valves' for the secondary boom function and see if either one of those are damaged.

According to one troubleshooting manual i'm looking at you can test the primary and secondary boom directional valves by swapping them and see if the problem follows/moves to the function primary, if so then replace the directional valve.
Also when you activate the secondary boom function if you get 2800 psi then there is an issue with the valves, it should not be that high if the cylinder is moving and not bottomed out. (follow the proceedure above)

First and foremost you need to have the correct manual for the serial number range of your unit so verify this before following my instructions above.
AND if you are unsure about any of this then by all means call a professional aerial lift tech. Remember safety is first and foremost and these machines are personnel carriers so they should only be repaired by trained service personnel.

Can you put a pressure gauge in the cylinder feed line? Maybe the cylinder is hydraulically locked due to a blown seal.