Ok, got it working and the solution was unexpected so I thought I'd post again just in case anyone else finds themselves with the same problem.
As you will have gathered from the first post, after installing it, I couldn't get MM (v5.1.3) to work with the internal GPS and I wasn't all that surprised as, other than the built in Google Maps and GPS viewer I hadn't been able to get anything to work. The nearest I'd come was with a freeware prog, NaviComputer, which worked after a fashion but froze on exit and seemed to lock out the internal GPS.
Anyway having installed MM and failed to get it to work on any of the available COM ports I decided in desperation to try configuring it using the external GPS settings despite knowing that this should have nothing to do with the internal set up. Knowing from GPS viewer that the internal was on COM 0, I used that and COM 4 and, miracle of miracles, MM got a fix. Mind you, none of the other GPS progs now worked and MM exited with an error locking out the internal GPS until I restarted WM.
There was only one thing left to try; factory reset.
Imagine my surprise when I re-installed MM and it now worked... I'd set NMEA, COM 4 and 9600 Baud and it got a fix, exited normally and didn't lock up the GPS.
Being a curious type I still wanted to know what had caused the original problem so tried to make it happen again by replicating the original set up. Everything was fine until I re-installed NaviComputer, set it up and ran it. After that it was back to the original problem.
Beyond knowing that NaviComputer didn't seem to get on with WM6.1 and MM I've no idea what the conflict is but at least I've got it working.
So, it seems that, if you have problems with MM on a WM6 device, you may need to do a factory reset then reinstall without any other GPS software installed (other than View and Google) and without touching any external GPS settings.