I’ve been using my DAW to sequence both my AR and my A4 and it’s been working really well.
Wouldn’t say that I’m using my Elektron gear as “sound modules” really. What I normally do in these cases is that I sequence in my DAW and when I got the basic stuff going I sync my AR to my DAW and use “live record” mode to record the midi notes coming from my DAW into the AR sequencer. (For me most of the “magic” happens using the Elektron sequencer features.)
Regarding your problem; I’m wondering if using the individual tracks corresponding midi channels when sequencing would help? Or perhaps your computer is sending very sloppy midi to your AR?