Sorry, this turned into a long post, but here goes ...
I have a similar and ongoing "problem" with my 430 loader on my 990. I put "problem" in quotes because it is more of a minor nuisance to me than anything, and I can bleed the air out with some cycling of the cylinders when it happens.
Here are the symptoms I see and how I deal with it:
Just like your issue, if I point the bucket down a little so the bucket cylinders are extended a few inches and then try to lift the front of the tractor off the ground, the cylinders will often push back in a couple inches when upware pressure is applied to the bucket lip, indicating trapped air. I can also see the lift cylinders bouncing in and out a bit when I drive over rough ground, also indicating a bit of trapped air.
Stroking the cylinders fully in and out several times will generally bleed most of the air out, BUT I have noticed that the cycling is much more effective if done at full throttle (more hydraulic flow available).
I think there could be a few reasons for air getting in:
First, low fluid level could cause the pump to suck air occasionally or lead to excessive foaming of the oil or something.
Second, heavy loads in the bucket can apparently cause cavitation, especially when the bucket is dumped. The heavy load tries to pull the bucket down faster than the pump can supply fluid to fill the void behind the extending cylinders and the vacuum created can cause cavitation and resultant air pockets to be formed.
Third, air could possibly be pulled in past the cylinder seals or even SCV spool seals. I think this might be possible under the same conditions as the cavitation mentioned above, and maybe if the tractor is left sitting idle for a while with the loader in a position where the lift arms or bucket can settle, or move a bit from their as-shutdown position.
In my case, it seems that drawing air in past the seals when left idle is the most likely cause because the problem is always worse when first starting up the tractor. I can get it all bled out and holding solid, park the tractor for a couple days, and when I go to use it again the air is back.
Here are some thoughts on bleeding the air out by cycling the cylinders, which I'll throw out for comment ...
If you lift the loader just enough to allow the bucket to be fully dumped and curled back, the dump cylinders are in a fairly vertical position. Imagine that there is air trapped under the piston, on the rod side. When you extend the cylinder in an attempt to bleed that air out, the piston moves down and at some point that air will get pushed into the rod-side hose. When the cylinder is bottomed out, you now have a hose full of air, plus whatever air is still in the cylinder (there will be a bit of space left in there even with it bottomed out). Retract the cylinder and that air is just pushed back in.
With the bucket curl cylinders, I always cycle them several times with the loader down low AND with it raised all the way up which puts the curl cylinders at a bit of an upward angle (rod higher than base end) in the hope that the air will keep rising toward the hose and eventually all get flushed out. You can't do this with the lift cylinders, however, so what to do about those?
I have read that hydraulic fluid will absorb air slowly under pressure and so with use all the air should eventually go away, but I have no idea how much use that might take. Perhaps the fact that, in my case at least, cycling the cylinders at full throttle works better is because the high speed oil rushing to the cylinder gets any trapped air all stirred up and suspended in small bubbles rather than allowing it to just sit under the pistons.
Well, those are my thoughts on the issue. Any other comments, corrections or suggestions?