Starting with 1.1, index.html has been replaced with 2 files,which are used depending on the setting of html.customNavigation:
If html.customNavigation=false then welcome-nav-template.html is used, which is similar to the old index.html, displaying the classic/legacy navigation design of perspectives and views.
If html.customNavigation=true then welcome-nonav-template.html is used, which provides a blank background with no automatic navigation design.
Note that as a result, html.compactNavigationTabs will only have an effect when html.customNavigation=false.
As I see it you have the following migration options:
For best results, use the Firefox browser..