Hello all,
To resolve the second above issue with the JDK, we have simply installed the Sun JDK, instead of the Open JDK. Don't let yourself be misled by the plethora of ways on Google you can apparently do this. We found this to be the easiest:
apt-get install sun-java6-jdk
And, to ensure that if there are multiple JDK's on your machine, select the right one using:
update-alternatives --config java
Or remove the OpenJDK:
apt-get remove openjdk-6-jdk
Of course based on the rights of your account on the machine, you may have to bump your rights using sudo.
Regards, Jeroen
On the partner portal you can download the 2.1 version of the mendix service, see also here
(Removed old answer, see the comments)