Hi Matej,
For the main_channel case you have specified right and left banks that have a length of 1 and set the "AlongChannelInterval" to 200. The AlongChannelInterval parameter defines the length of the element edges along the channel. You'll have to provide either longer banks of choose smaller elements.
The same holds true for the side_channel case where you provide banks of length 0.3 and specify an AlongChannelInterval of 60. In this case though I seem to have missed some basic error checking that results in BlueKenue crashing. That is "mud in my eye" indeed.
I will report this bug it to Alan Barton at the NRC.
Hope this helps... Martin