Whilst I can accept that mechanical losses should be low in theory by comparison this doesn't explain why my pilot believed he was having to put in a lot more effort to maintain the same speed/power on the front of his tandem as opposed to his single bike on the turbo. Maybe power was being lost having to drive the rear cranks around on his own but I can't think that would make such a difference. The other mechanical losses could be through chain strech/tension in the link chain but again, I can't see that being much either. Any other ideas?
I do still believe there is a much bigger loss through teams not riding well together. If anyone's not convinced of how significant this could be you can take it to it's limit and just get one rider to stop peddling. And if there isn't a signficant loss, why won't a tandem go up hills as quick as a good climber on a single bike. In theory, you've got less than twice the weight of 2 single bikes + riders and if no significant power loss, twice the power. So it should be faster. I don't care who you put on the tandem, it will never climb as quick as a good single climber.
Another way to think of it is that on a single bike, if on your trailing leg (the one coming up) you do not feel pressure on the top of your foot or feel any pressure on the base of your foot, part of the force you are exerting on your leading leg is being used to lift your trailing leg. So even on a single bike, if you are not peddling in perfect circles which nobody can, you're resisting your own force at some point in the cycle. When you add another person into the mix, the affect will be exaggerated.
The laws of physics dictate that if one ride is exerting more force than the other, they will be trying to accelerate the entire bike for however long that unbalanced force exists. This will be more fatiguing than on a single bike where you are only tring to accelerate your own weight.