Thanks Gentlemen for the great response. I have ordered the parts and will give an update when repairs are complete.

I would almost positive that repacking the cylinder, and while apart, replacing the cushioning valve in the bottom of the center lift cylinder will cure your problem.

Packing or valves in primary lift.Order both to be safe.

i still think its a dry or binding carriage rail (maybe bad side rollers)
but ive seen those valves go bad (in the piston rod not the fitting) and cause odd issues

so i was thinkin of the right thing but the wrong function :( lol

If you had a problem in the down safety valve, the fitting on the left side secondary cylinder you would not have a staging problem, rather the carriage would lower slowly. That valve is to provide a metered flow that prevents the mast from crashing down. Note that the down safety valve is not a velocity fuse,that will stop the carriage completely, so if you were to have a broken hose or line you would get a mess. But that is not the problem in your case.
But also check for binding in the carriage or mast rails.

It sounds like you have a leaking up-stroke cushion valve. (Not a down safety valve) You will need to disassemble the free-lift cylinder and replace the check valve in the piston. If it leaks you will get fluid build up on top of the piston, it takes more force to push it out the check valve than it does to raise the inner mast rails, that is why the second stage cylinders will fully extend before the free-lift cylinder has enough pressure to force fluid out from the top side. This problem happens under normal conditions if the operator makes quick partial lifts. Under these circumstances fully extending the mast corrects the problem. Since it happened again I believe you need to replace the internal check valve, you will also need a free-cylinder packing kit since you need to dis-assemble the cylinder. I have had a problem where the check valve retaining ring (snap-ring) broke, thus causing piston damage. I needed to replace the piston also.

oops my bad
it is in that fitting
im not sure which mast im thinking of hmm

If you fully stage the mast you notice it will correct the mis stage problem, replace the fitting in the bottom of the primary lift cyl.

The hydraulic fluid will follow the past of least resistance so if the packing is bad in one of the side cylinders the fluid will go there first before the free lift cylinder. On a lot of "foreign" trucks there are tubes at the top of each cylinder that return to the tank. If you take off the tubes raise the mast all the way up and keep hydraulic pressure on it once it has reached full extension there should be no fluid coming out of the tube ports. If there is then the cylinder in leaking internally and the must be repacked.

grease the mast channels
they might be dry

dont use too much just get a thin layer on 1 side of each channel that the carriage rollers go in, the rollers will transfer the grease to the other side of the channel
too much grease can stall the rollers and cause damage to them and the mast channels

also make sure the side thrust rollers arent loose or broken and may be jamming up the works (again in the carriage)
theyre held in by 2 bolts each and they have grease fittings too

look for anything binding the free lift cylinder

in the bottom of the the piston rod itself there is the valve that limits the flow of fluid that can escape if the line loses pressure (burst)
maybe that has an issue

good luck

I think it is best to state what the problem is or was first.