I think I'm starting to get to grips with this now (haha, famous last words!)
Running the VB straight from the .exe works MUCH better than within the IDE, and here's why...
To see what's going on behind the scenes Debug.Writeline is really handy, HOWEVER, dumping text into the immediate window really slows things down and seems to interfere with serial comms particularly badly, especially when there are lots of lines being returned in quick succession. The immediate window seems to insist on reporting everything as effectively as possible (which is fine in itself), but it seems to lend so many resources to printing and scrolling the outpouring of text that it will happily corrupt the transmission of serial comms and leave you wondering why something so simple often falls flat on its face.
I have now removed all of my Debug.Writeline command and now use StreamWriter to populate a text file with all of my event reports, and things are running so much better. I would like to say perfectly, but I'm still cautious (and the connection to my X-actuator has fatigued-away after performing over 140,000 transits over the last few days!)