Hi Muntasir.
Problems appeared after updating the old 1.1.4 template to the latest shaper_ultimate template (update from Joomla backend)... (my changes to the original template were only in custom.css and main.js)
After updating the predefined headers are missing and custom.css isn't loaded. I've tried turning the compiler on and off, emptying the cache, etc... with no luck.
I managed to reinstall my custom template with overwriting files from the new 2.0 template, but .ini file needs to be added manually. After fixing all, the only problem I've experienced is having a problem with not loading custom.css.
When I replaced the index.php file from the rc2 version all is fixed and custom.css is loaded correctly...
Hope this helps...