I looked into the issue a bit deeper and found the rreason why my devices 
stopped working:
I had all my local rules in files like 
50-avrprogrammer.rules
or 
50-cm.rules.

The "new" libusb-rule has moved the permissions for device-type "usb_device" 
from  
40-basic-rules to 50-udev-default.rules.

Suddenly my rules are applied _before_ the default-rules, therefore all
permission settings I made are invalidated by the default rule .

-- 
udev rules for libusb revokes permissions from normal users
https://bugs.launchpad.net/bugs/374245
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