Alright,

the new version works much better than the first one.
With the new receiver the problem of the charging being interrupted after some time is gone now. So far I successfully fully charged my N900 two times.

Though, there is a slight new "issue" the charging process is slower than via a USB connection to a PC right now. Afaik the problem is caused by the forward voltage drop of the diode.

Due to this the voltage on the battery side is smaller than 5V. Actually, the new Powermat receiver (Nintendo DS Lite) I am using supplies about 5.15V. Though, due to the diode in the circuit at the N900 USB side the voltage is lower. I already use Schottky diodes as these have the smallest forward voltage drop.

There are some solutions using a (MOS)FET instead of a diode which should result in a significantly lower voltage drop. Though, I am not that much into electrical engineering topics and didn't try this yet.

I'll keep you updated...