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.