Yep I have this. I contacted Elektron about it and they told me it is an issue that they are trying to resolve in the next update.
If you look closely the “play” button on the DT will stay green when you stop the sequence. If you stop it from the DT by double tapping stop then you wont have a problem but stopping from an external sequencer wont reset the sequence completely. I had this with my OT and E2S and then I contacted Elektron. They told me to use the DT as my master and slave everything from that which is really annoying