Thanks for your suggestions!
I've soled it by using 4.3 and a custom FFMpeg build mentioned here:
https://www.raspberrypi.org/forums/viewtopic.php?t=227359
Works fine and without hiccups.
@CvH: Is it sufficient to make a backup from the LE Config tool or do I need to DD the complete card if I want another copy of my LE setup regarding the TvH plugin?
EDIT: could this be the culprit I'm facing with 4.2.7 and the hiccups?
(gkreidl in the mentioned thread)
Transcoding on Jessie is more efficient though because the gst-omx module has implemented hardware scaling, which is missing in the Stretch version
As soon as i set '-vf scale=720:576' I have the same hiccups as before.
Will try the whole thing on Jessie soon.