That is very strange. I've never had that happen, and I've hibernated a lot of tortoises in the fridge. Are you sure it is 41 degrees? Some thermometers can be off by 4 or 5 degrees, so I would double check using another thermometer. Can you hear him moving around a lot? Some tortoises move even while they are in hibernation every once in a while and this is no problem, but constant moving around and scratching is sign of something wrong, and it's usually too warm of a temp. I have commonly seen occasional movement, but I have never seen a tortoise's eyes remain open. He may just be opening them when he feels the vibration of you opening the fridge door or moving the box and then closing them after it settles down.
If it really is 41 degrees and he is truly not hibernating, the only thing I would sugest is that you bring the temp down a degree or two. Tortoises can hibernate just fine at any temp above freezing. The thing is, you have to be very certain that your fridge is responsive to the temp control and will not go down below freezing if you try to lower the temp just a smidge. If you do end up lowering the temp, be very sure to check and re-check the temp for the next couple of days to make sure it doesn't get too low.
Also, you can take him out and see what he acts like. If he starts walking right away, you have problems. A hibernating tortoise should remain fairly still with it's head in for about 15 or 20 minutes after you take it out.