I've had no trouble keeping water in those clear screw-top gallon bottles at home (those bottles are slightly better than milk-type jugs, but only slightly). However I've had similar leakage problems with any type of gallon jugs in my car, including some pretty tough $5 jugs. I gave up on large containers and switched to buying 24-packs of 0.5 or 0.7 liter bottles for the car and have had no problem with those. It turns out to be convenient, I don't reserve them for emergencies, I just drink them when I feel like it and replenish them, so I don't need a rotation plan.

I think it doesn't take much temperature change to make you lose water from large bottles. It's more a matter of hot temperatures than cold. My guess is hot weather pushes water vapor out of the bottle. The bottle them collapses when the weather gets colder.

For long-term storage (more than a year or so) it's supposed to be best to use sealed containers like Aqua Blox. Those supposedly have a 5 year shelf life.

In fact I had a 1 liter Lexan camping bottle full of water in my kitchen for 2+ years (not an intentional experiment, just didn't use it for that long) and I decided to check it and it smelled and tasted just fine. I poured it out anyway and would want to have some kind of purification device around if I were to store water that way.

For home storage of larger volumes, I'd look into this: http://aquaflex.net/
I haven't tried those things though, so don't know what the pitfalls are.