Are there other explanations for slow tyre pressure loss? I rode my road bike on Friday and the tyres were at the correct pressure then, around 100psi.  On Tuesday, I jumped on without checking them and quickly realised something was wrong with the rear tyre.  It wasn't completely flat but was fairly soft.  I hadn't gone far so went home and took the car to work instead.  When I got home later, I was surprised to find the tyre, while still soft, hadn't lost all pressure by any means.  It was around 40psi and felt the same as when I left it in the morning.

I decided there must be a slow leak somewhere, but I couldn't find one anywhere, putting the inner under water and going around it methodically looking for bubbles.  I've never failed to find a leak before that way.

I've switched it out anyway because I don't want to mess around with my commute, but I'm curious ... is there another explanation for that amount of pressure loss?  Or must there have been a puncture somewhere that I missed somehow?

The tyres (whole bike) are pretty new and in excellent condition.
Could be a faulty valve that only leaks under high pressure.  You won't be able to find this kind of thing by putting it under water because there's no way you'll get the tube up to 100 psi while it isn't on the rim with the tire on.  It could also be due to very very small holes in the tube, again which don't make any difference until the tire is at very high pressure.  You may be able to test this if you fill the tire up to full pressure and then leave it in the bath tub or other large sink.  you should be able to see if air is escaping from the valve this way. Not sure if you would be able to see air escaping from very small holes in the tube though as they might not be visible due to the tire/rim.