The problem is solved, it was not Joomsef ;)
A firend of mine checked the site and code and found out that i was hacked :(

We reupped an old, clean backup and all is working well again :)

the problem is still present :(

The Dropdown menues are back, the site is not without a index.html redirect to www.iptaichi.de/startseite ...

I also used Purge SEF Urls, Clear cache, Update URLs but to no avail. the only consequence I got was that now not all dropdown menus show up when I mous-over them, and instead lead to 404 Pages.
Here you can see for yourself:

www.iptaichi.de/startseite

(except for "Shop" all should havea dropdown menu)

Any ideas?

Generally I like Joomsef, it worked fine for about a month. and "decrypted" the web adress nicely. now, however, the website wont load anymoe if you put in the blank domain name www.iptaichi.de
when I use this www.iptaichi.de/startseite it loads well.

So I use a workaround for now. I deleted the HTML redirect from my .htaccess and wrote a litte redirext index.html that links to the working link, but I would like to have it in normal working order again. Any help here would be appreciated. Deactivating does not revert the site to the former working, cryptic links...

Also, I want to take the categories out of the SEFed links, but it does not seem to work.

Here is my .htaccess if that is needed:

DirectoryIndex index.html
RewriteEngine On
RewriteBase /

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$ [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]

########## Begin - Rewrite rules to block out some common exploits
## If you experience problems on your site block out the operations listed below
## This attempts to block the most common type of exploit `attempts` to Joomla!
#
# Block out any script trying to set a mosConfig value through the URL
RewriteCond %{QUERY_STRING} mosConfig_[a-zA-Z_]{1,21}(=|\%3D) [OR]
# Block out any script trying to base64_encode crap to send via URL
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [OR]
# Block out any script that includes a <script> tag in URL
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%3E) [NC,OR]
# Block out any script trying to set a PHP GLOBALS variable via URL
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block out any script trying to modify a _REQUEST variable via URL
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Send all blocked request to homepage with 403 Forbidden error!
RewriteRule ^(.*)$ index.php [F,L]
#
########## End - Rewrite rules to block out some common exploits

I was thinking about buying the pro version of joomsef, but only if this problems can be fixed.

Best,
Sascha