About your reply.
1. Backup/Restore. The main problems appears to be from 1.9 (upgraded) to 2.0. It means, the courses on the moodle 2.0 that are there in an upgrading process from 1.9 to 2.0. I did a backup/restore for a new course (but with a few materials) and it have worked fine. I don´t know if it was a matter of the simplicity of the course or because it was a backup/restore processo from a courses created in 2.0 to 2.0. I will test more.
2. Image files missing. I´ve found this "images missing files" in a all brand new 2.0.1+ installed site (not upgraded from 1.9). The image files missing is related to themes (all, including standard). In Apache log it appears clearly. In IIS log I have in addition the time that the server stays with the error (1 to 3 ms for each file missing, usually 10 files missing). But a regular click for a navigation last for 2000 ms and more the first time. After loaded, it´s fast. Missing files appears to be an easy thing to fix, but the current navigation code is a major issue. I don´t know, maybe a true AJAX strategy (downloading a xml navigation file right the way the user logs, checking versions in case of not changes) could be a way for a solution.
Neverthless, I will keep tracking the 2.0 evolution and will go 2.0 as soon this issues had been improved. For a while, I should stay with 1.9. (I´m sorry having no time to help more in improve it).