1. Are there problems with copying / using defaults.jap, created on a Linux installation, to Windows?
That file shouldn't be much of a problem, but others might be. In short, the problems that do crop up all involve the paths. In defaults.jap, for example, the MyAlbums location is specified, and the path isn't going to be compatible on two different platforms. In project files, you run into problems if you've specified an output directory location other than the default album. You get the idea.
The easiest thing to do, rather than copying files, is install jAlbum on the Windows machine, then import settings from an existing project that used the default settings. Then save as default. That will avoid the path problems.
And if you're opening an existing project, take a good look at things like the output directory location before you make an album. If you don't, you'll end up with some stuff in weird places in the file system, as jAlbum struggles to make sense of the path.
2. Is it possible to have two users on one install - so the second one does not "mess up" settings, etc? Or, must one get a second license?
If you want two users to be able to use jAlbum on a single Windows machine without bumping into each other, you need to login to Windows as two different Windows users. Login as the first user and install jAlbum. The config files will be planted in C:\Users\userOne\AppData\Roaming\jAlbum. Then login to Windows as the second user and install jAlbum. That user's config files will land in C:\Users\userTwo\AppData\Roaming\jAlbum.
I won't swear to any of this, because I have never used Windows in a multi-user way. There may be some complications I'm overlooking.
You can both use the same jAlbum username, and share the license. No collision problems as long as you're not both uploading to the same jalbum.net storage space, and even then there's no problem unless the two users happen to use the same project name.