There's already 10.4.1 since yesterday - maybe give that a try.
Same here. Both in 10.3.1 and 10.4. For me, it occurs every now and then, but mostly when modifying Grid 2. Do you recognise that?
When you get the message, indicating the application is already open, you can validate that you don't accidentally have another MxStudioPro open. When not, click the ignore button to proceed.
The message is triggered by a lock file, set when starting MxStudioPro and removed when closed. The lock file isn't removed when you don't shut down gracefully. When starting a new session, it is detected. The ignore button continues the session. Two open MxStudioPro changing the same database could lead to unexpected behaviour and inconsistencies.