I have been wrestling with this problem on and off for over a year now.
I realized something today - that was just a total "well of course, why didn't I think of that sooner?" moment.
In ableton - check your midi routing.
By default - it will accept "all ins" on "all channels" - and monitoring is set to "Auto" for your midi track.
The result is - you create a midi feedback loop from the seq/arp - and it does whacky stuff with the clock.
What happens is this:
when you start playing, the SEQ/ARP will play a note.
That note gets to sent to Ableton on midi channel 3 (by default).
Since the midi track is monitoring "all inputs" on "all channels" - it sees that midi note come in on channel 3 - and immediately routes it right back to the MF on channel 1.
That not only kills your SEQ/ARP sequence, but does whacky stuff with the clock, and the BPM - since the messages are bouncing WAY faster than normal midi msgs would send/recieve. I had my BPM reading at 600 something at one point, even tho it was set to 130.
This may or may not solve your specific problem - but I've had very very similar issues seemingly randomly - depending on what other gear I'm using. I've somehow missed it for ages and just now realized what was happening. I had another synth armed for recording in ableton, but nothing playing on it yet - and when I started with the microfreak on, suddenly synth #2 was playing the same arp sequence as the MF. Had kind of a "oh god how could I be so dumb?" moment, and things suddenly made sense.
Hope that helps.
On a side note - also be aware that if you're using midi over USB - there's issues there if you're running thru a hub. I also HIGHLY suggest not powering thru USB, especially if you're using a USB hub, as the power can be inconsistent and that does really weird things, since the voltage isn't always what it needs to be. Your filter and some other params may go highwire and be uncontrollable. Since ya know, voltage controlled params...
