I looked at your screenshot,
first you have to connect Spark Private In to the instrument not Spark Public In.
The MIDI learn should be saved in a preferences file so this is the same for all presets.
If it does not remember the mode of the filter it is a bug. I will check it.
Concerning the pattern change record, this may be because you record the data from the controller (Spark Private In). The data should be sent from the software to the IAC driver then recorded into Logic from the IAC driver (see this video
for more details).