Okay, I progressed a bit.
First maybe some background. I'm not completely new to PMAC, but haven't worked with it for some years now (and even then wouldn't have called myself experienced). Currently I'm taking over a project started by somebody else, which drives a lot of stepper motors using a PowerBrick LV. Firmware version is 2.4.0.180, IDE used is 4.5.1.3. The project itself seems to use both approaches from the v3 and v4 worlds. The motors are configured using Global Includes, but the systemsetup.cfg is used as well.
First issue was, that the IDE was not downloading the files properly. I don't really get it, but doing "Build and Download All Programs", save and $$$ always left me with a differing project on the controller. At some point "Build and Download All Programs" did not even reach the point of downloading the files any more and I restarted the IDE. That helped.
Still the clocks were not configured in the same way, because meanwhile I tried starting from scratch, with a clean project in which I copied the config - being not aware of the way systemsetup.cfg is created.
Then I spend quite some time struggling with the systemsetup.cfg. No matter what I wrote to that file was reverted on downloading it. The set of manuals I used had the same creation date as the IDE, but none of them only mentioned the existence of systemconfig.cfg. I was able to find the information in the forum, that the file was created by the setup wizard - but this does not exist in version 4.5. Discovering that I had to double-click the colored boxes on the CPU->System page to change to config was not what I would call intuitive. It's explained in the most recent version of the IDE's manual, which I found only after solving it myself.
Still, the second and more important issue remains. Issuing a jog command would just cause a jittering following error, otherwise nothing happens. The "Troubleshooters" are all green. Maybe it's not connected to the clocks. But as the motor config is done in the Global Includes and was working fine on the other controller, it leaves me puzzled.
Any ideas?