Might still be worth a try. It's the frame view for the books that isn't working. If I go to a frameless view things seem to work; not well enough to read easily, the font is too small and can't be resized, but it suggests it's an incompatibility in the browser, not a feature of GoodReader itself.
I also sprang for the HTML Presenter app. Kind of a pain, since you have to package the HTML files as a .zip file and sync through DropBox (files are local after the sync). It works exactly like GoodReader. That suggests the problem is a WebKit problem.
HTML Presenter seems a bit buggy, btw. There were other inconstancies, minor but annoying, that forced me to clear it from RAM and restart.
I've given up on porting the HTML books to the iPad, for now. Just reading then on the computer. (sigh)