On my problems with Great Generals, I've 'solved' it. I just deleted the ROM-AND folder and re-installed it from the latest SVN, I've downloaded, and it fixed the Great General problem. Fixed also Great Generals and Commanders, getting only a generic name, and not being named after a Great leader in history.
I think what happened, is that I've used a downloaded copy of the full SVN install to install the Mod I'm playing, and it was somehow corrupted slightly. I tried to re-install from that Saved full download, but it wouldn't load. So I deleted the installation, the downloaded copy, and just used the updated SVN version, which is the full SVN, checked out and updated.
I'll have to try from a full reload, but it should work fine now.
I've one other problem though, I'm playing a high to low game, and now I'm on my 3rd Civ, but my ORIGINAL civ, went back to being minors, and they are researching INVENTION.!!! I wasn't a minor when I left that Civ, I was a MAJOR power on the 2 continent world, but left it with some rebellion issues. (which didn't work as I hoped.)
The 2nd Civ I've left, on the other continent, didn't revert to minor status, liberated some cities to the rebellion problems I left it with, and has been at war with them, vassalled other minor players etc, so is working fine.
The "Minor" civ, has maces, Crossbows, Pikes (I left it with Pikes) etc. So they have been able to research advanced Tech's, capture cities, build Treb's etc.
Its a bit of a Disappointment, as its where I captured my Capital city from 1st thing.
Not totally game breaking, but not in the spirit of the game.
On Amphibious assaults, I've seen it happen, not too Often. I think they need to originate from a coastal barbarian city, not just from the dark, so that Barbarian city, needs to build the Galley, ship unit, assault units, then send them off to attack with the naval path finder, so a bit convoluted path of logic for it to follow, overland would be much easier.