Indexhibit Support

Hello. When upgrading to version two everything seems to be working just fine. After couple minutes my site shows:
404 Not Found
The server encountered an internal error or misconfiguration and was unable to complete your request (...) More information about this error may be available in the server error log.

Error Log (from host):
24.06.2015 10:35:59 peterschaefer.net [client 2a01:238:e100::] malformed header from script. Bad header=Not Found: index.php

Anybody a clue what could be the problem?

peterschaefer.net/

Hello. After following the upgrade instruction over again the mentioned Error does not occur any longer, but now the menu seems to jump from html to css style? Sorry for being a pain, but I am a bit lost here for the moment. Any guidance is really appreciated. Thanks.