I'm a mechanic at a Kubota dealer, fitted a 60" deck to a BX25 today. The problem you are having with the height adjusting knob is not uncommon. We often find that straight out of the crate they will not lock in and need a bit of adjusting. And if you try to calibrate the deck cutting height to what the knob says you will be disappointed, they are never accurate. You might set your knob to 2.5 inches, but the true cutting height between the blades to the ground will be more like 3.25 inches.
The more you screw those 2 adjusting bolts on the lift links down, the higher the relative deck height will be to the machine's lift arms. So when you raise it right up the deck will butt up hard against the chassis and stop the locking cam mechanism from working because the lift arms haven't reached the top of their stroke yet.
To fix this, you need to forget about the accuracy between what the knob says and the true cutting height to the blade tips to the ground, you will never get it right, you might get it close if you have turf tires which lowers chassis/ground height, but your BX25 will have industrial tires standard so the chassis will sit higher and throw out the calibration of knob height to true cutting height.
Firstly disconnect the rear lift arm links from the deck. Raise the 3PL to it's highest position. The height control knob should be able to lock in to the TOP position. If it doesn't then you need to make an adjustment to the lift rod adjuster behind the Left Rear wheel. Screw the adjuster bolt in a bit and try it again, this will raise the lift arm shaft a touch relative to the 3PL position and give it a higher point on the cam lock pin and should lock in to the TOP position on the knob. If it doesn't, screw the adjuster in some more until you get it.
Next, make sure your rear tire pressures are the same (22psi) and have even tire wear otherwise the machine will tilt to one side or the other which majorly changes your cutting height from left to right spindles.
Park the machine on level concrete. Reconnect the deck to the lift arm links. You need to back off those 2 adjusting bolts on the lift links to allow the relative deck position to lower in relation to the lift arms and keep it off the chassis. You need to lower it down just enough so when the 3PL linkage is at it's highest point the mower deck is just touching, or about to touch the chassis, they should never be butted up hard against the chassis otherwise it won't lock in TOP. Your height adjusting knob should click into the TOP position. If it doesn't then you might need to adjust the rear bolt in a bit more.
Once you have achieved your TOP lock in position, you can then lower it down to approx 2". There is a special blade height tool you can buy that you insert from the outside of the deck and a telescopic arm reaches underneath and touches the blade so you can compare the left blade cutting height to the right blade. If they are out, you need to loosen the adjusting bolt on the lift link of the HIGHEST side, never tighten the lowest side to bring that side of the deck up because it will just hit the chassis when raised again and cause the original problem again of not locking in.
The last thing to do is set your height knob to where you want it, and then adjust the height of your anti scalp wheels so they run 1/2" off the ground.
Just remember these mower decks are not a precision work tool like a golf course cylinder mower, so unfortunately with these "near enough is good enough" as long as the blades give a level cut then it's what you want and ignore what the knob tells you because they are inaccurate.
