Re : Two problems: top_bar.tpl and image thumbnails
Hum James it looks like you have something not quite standard, I didn't have to mess with any of this stuff to get it working on EasyPHP or MDK 9.2 Advanced Extranet Server.
What's your version of GD?
This page gives information about the jpeg-6b support, particularly --with-jpeg-dir=DIR.
Try to come on #tikiwiki (or even #php) if you can, maybe that can help.