Why do I go through laser cubes?
The tractor beam only causes collision problems when the player leans on the cube on the wall while in the tractor beam.
Ok, I have it sitting on a button on the floor with the tractor beam there. Thanks for the information. I think I can set up some timing so I can fix it if thats the problem.
Laser cubes become ghosts (ethereal) when they are pushed into or near a brush with a funnel. They can still activate buttons and be pushed with other cubes but you cant push/jump on them. Its a bug.
Happened for me too when a funnel pushed it into a rotating panel.
Also rarely happens with normal cubes, but with them its the opposite: in my map #1, there was a door what was set to force close and do damage if blocked. If a storagecube was in its way, it just pushed it away but probably partially "killed" the cube, so it was there, but when placed on a button, nothing happened.
Laser cubes also act weird when a laser goes thru them, it "freezes" them, so for example if you try to push them with a moving panel or func_door, they just go thru it (or they float when cubes/platforms are moved from under them), but if they are not activated, then they are pushed properly (so when you want to move an active cube by any mean, you must turnoff/turnon the laser for 0.1 second).
Laser cubes are very bugged in Portal2. To prevent the ghosting, remove any func_brush (even if they are arm/panel attached brushes) from a funnel's way (funnels force to push the cubes, maybe thats the reason).
In a map I started to make 1.5 year ago, the same thing happened in a test 100% of the time, and had to abandon it because of this. Failed to find any fix. I may continue it with a workaround, where the cube gets fizzled and a new one will be dropped, soe the player will never retrieve the ghosted cube, because the next part of the puzzle is about jumping on it, which is not possible when its ethereal. 
Try using the ExitDisabled state on it right before pushing it with a panel or whatever.