Hi Nik,
I've personally had some issues with Ubuntu, but i'm far from being able to say for sure that's the problem. Still, i suggest trying Fedora or a Windows host for Mango to see if your serial ports stick around longer.
Also, make sure data sources and testers aren't competing for the port in the case that you have multiple data sources running. Only one running data source can own a serial port at a time. Note also that the node scanner owns the port while it is scanning.