First of all, awesome piece of work. I finally got myself to play with the editor some more, and while I don't have any bugs to report at this stage, I have a few comments/suggestions:
256 building limit
I predict this is a lost cause, because as Keroro said, it looks like the phantom resource problem. While you can have a lot of them, the variable that indexes them in-game is limited to 32 and then overflows, if that's the right word - so every resource X is treated also as resource X+32, X+64 and so on. The pattern is different here, but it looks like the reason is the same.
Landmark tundras, jungles etc.
They work, as explained
here. Again, I added them by manually editing the data in the BIQ. Civ3 editor properly reads these new landmarks and can edit their stats - why not give the option to enable them in your editor as well? Of course, given that Civ3Edit map editing becomes a problem and LMs have to be placed with hex editing again... it'd have to show some warning when you try to enable them them.
Master file
I like this idea, although I'd also recommend saving it for later, when the basic editor is done. It would help a lot with creating sub scenarios, even if it's only for civs. The way I see it - have say, 40 civs in your editor, select 31 "export" ones and hit export.
Barbarian cities
I've been experimenting with them long time ago just by hex editing the BIQ and got same results - it worked fine in the editor, but the game would always remove the cities at start. Yesterday, I decided to use your editor with Skyer2's exe hack, which enables barbarians to capture cities. And the good news is, it worked! The problem with Skyer2's hack, apart from the fact that it only works with a cracked exe, is that it looks ugly (no city graphics, or leaderheads instead of cities...). With your editor I was able to fix that problem. So now barbs have nice looking cities and build new units in them, even settlers. The only remaining problem is that they don't seem to use Defensive unit strategy and leave their cities unguarded and mostly unproductive because of resisting population. Anyway, I'll play with this a bit more and see how usable this can get.
Civ limit
Would it be a lot of work to enable adding of civs beyond the 31 limit, for testing purposes? (since another Skyer2's hack allows increasing the civ selection number in game beyond 31).
Bonus resources & appearance ratio
Another experiment suggestion - enabling the appearance ratio for bonus resources.
That's all for now
