Meanwhile things become a bit more clear. Reading a GPIO DATAIN register harms the timer, writing data to some output GPIOs does not have any influence.
The problem can be reproduced easily with the DMTimer-code shown in http://e2e.ti.com/support/embedded/starterware/f/790/t/324059.aspx , when there reading of a GPIO input is added to the main loop (after configuring it properly of course) the DMTimer no longer works stable but comes with a big jitter.
So after I could not find any GPIO parameters in TRM that would explain this ... what could cause this behaviour?