What is the "Has Collide Box" sector flag and why is it added to every sector in my level? Also, what is the "texture flipped" surface flag and why does it randomly get checked on some surfaces in my level?

Not sure about has collide box, I don't think it matters. Texture flipped will mirror the texture. It gets applied when you copy, paste and flip sectors.

Re: copy/paste -- is this intentional or just a bug in Jed?

It's intentional. If you mirror two sectors, the adjacent surfaces will match. Stitching will set or unset the flag.

More information on collide box and other sector flags:

http://jkhub.net/library/index.php/Reference:Sector

Bleck. I have been using copy/paste to duplicate sectors because there is no [Insert] key on my stupid mac keyboard. Now I have a bunch of textures flagged "flipped" - and stitching to them doesn't seem to clear the flag. I have to stitch to them, notice that there is still a visible line, and then manually clear the flag. Once I clear the flag, the textures line up.

That's odd, I was pretty sure stitching would set the flag. Could be a bug where it does not. You could just multiselect all your sectors and uncheck the flag.

Will that also clear any other flags? I may end up just leaving them or doing it by hand if it will take too much time.

I mean multiselect all the surfaces. If you do that and then click on the surface flag box, and hit enter, it will set the flags on all those surfaces to whatever is in the text box. So yeah, it would clear them.

Might be able to do a 'Find' by material, multi-select, and then uncheck the flag.