I was able to solve the issue myself.
Somehow, the .htaccess File that comes with SilverStripe isn't compatible with all Apache Versions or doesn't work on all configurations.
This was running on a subdomain eg. http://sub.somedomain.com
Original rewrite rule:
RewriteRule .* sapphire/main.php?url=%1&%{QUERY_STRING} [ L ]
Which i replaced with
RewriteRule ^(.*)$ sapphire/main.php?url=$1 [ L,QSA ]
It does basically the same, i just rewrote it with my limited mod_rewrite Knowledge. $1 is the match from the rewrite Rule, the QSA flag keeps Query Strings and sends them to the rewrite "Target" as well. Maybe i should file a ticket for this...
After that, iFrame Fields were showing up nicely. The base href tag was broken on all these pages though (same goes for urls with action and parameter, eg. with multiple slashes)
I fixed this, by adding the following Line into my _config.php file (in my setup it was located in the mysite folder)
Director::setBaseURL('http://sub.somedomain.com/');
Replace http://sub.somedomain.com with your domain :)
Hope that might help somebody.