Seems that this was a newbee error. I had the example flow still active in the project, and used a second instance of the websocket in my own flow. But seemingly, those instances conflict with each other causing only parts of message to arrive.
If I have only one instance of the listening websocket in the project, everything seems to work smoothly.
The firmware upgrade problem, however, remains. I have fw 5.58, the OS has upgraded the firmware package to 5.60 but I can't upgrade the actual firmware as the fwspi --auto command doesn't start the upgrade.