The way it currently works is that the program change is sent as soon as the clip is armed (vs when it actually starts playing like normal). This is how the device gets around the program changes being sent too late.
So if your pattern on your Elektron is 4 bars long but your clip isn’t supposed to change until 8 bars, it will still arm and send the program change at the beginning of that 8 bar clip in Ableton. Meaning it will switch the Elektron pattern after 4 bars (if that’s how long your Elektron pattern is).
The safest way to keep patterns in sync is to make sure your clips are quantized to the same length as your Elektron patterns.
If you can’t extend your Elektron patterns then you may have to make duplicate scenes for as many times as you want that pattern to play (if you’re using follow actions). Your follow actions would just move to the next clip and send the same program change that is already playing so it wouldn’t change.
This is a current limitation because I haven’t create a way to deal with it.
I will put it on a list to add it to the new version when I create it. I need to go back and re-make most of the Arrangment part due to some new features available in the Live 11 API. Not sure exactly when that will be but it will happen hopefully soon-ish. I have 2 very young sons and limited free time right now.
I’ll either see if I can get information about the follow actions from the API or I’ll add some kind of manual “message” you can add to delay the program change in a clip.