The way I find is most easy is to hold the spring bushing down with a screw driver, and at the same time I have my other hand on the other portion of the gearbox, holding down the cylinder. As you put the two halves together, put your index finger through the cylinder slot, and use that finger to hold down the cylinder when you have the two halves nearly together.
In some boxes, (I find this most common in ics mp5 boxes) the integral bushing for the anti reversal latch is sometimes cast from the factory with a slightly larger bore diameter. This creates significant slop in the anti reversal latch, and when its under tension from the spring, it almost always tends to come out of place just when you are trying to get the box together.
When you do get the two halves together, check all of the axles, and anti reversal latch to make sure that they are where they should be. If they all seem to be lining up, but somthing that you still cannot see is preventing the closure of the halves, then it could be the slide rails on either side of the piston. Somtimes the spring will cause the piston to rotate slightly when you are assembling the box, and these rails will not line up with the rails in the two halves. This can easily be dealt with by either rotating the cylinder by hand, or taking a small screw driver, pushing it between the two halves and using the tip to rotate the piston one way or another.
Also, when Im getting things back together, I almost always tap on places that might have missalignment issues. Just turn you ordinary screw driver around and give a couple of sharp taps whith the back of the handle where you think may be causing the problem, and it should just pop together after a few tries. It almost always works for me, and sometimes you actually need to do it just to make sure that everything is seated right.