Hmm... interesting. I'm looking at one project where those jpgs are 261 x 398, but then I look at a different project and they'e 1042 x 1591! The bizarre thing is that both projects are made with the exact same page template! Weird...
Though, I still wouldn't consider 1042 x 1591 to be "print quality".
No, but it is good web quality. It might be something in your page settings. My thumbnails are of the 261 variety, but I would not be surprised at all if there's an option to go larger.
Another thought might be general page resolution. If one project is at 600dpi and the other is at 1200, perhaps it's a percentage of actual page size.
It looks like it's a preferences setting: under "story" there's an option for "thumbnail resolution" and you can choose either "standard" or "high". Probably at some point I stumbled onto that setting and messed with it... which is why I have some small ones and some large ones
Also, there's this long one from Dave Gibbons that is good, (it's a sponsored webcast rather than a tutorial, but covers a lot of the features)
You can pretty much search YouTube for "Manga Studio tutorial" and get a ton of stuff, maybe just watch out for the ones that are speedpaints if you're trying to learn specific things. Sometimes those are more entertaining/inspiring than instructive.
My Daily Drawing Blog
Here's a quick Manga Studio question: Can you make the panels and captions, lettering, and dialogue balloons before you do the artwork? That's how I do my regular comics on bristol board, I do the lettering first, drawings last.