It all starts at Vd - the design dive speed, which is based upon structural analysis: the big issue here tends usually to be structural integrity of the wing under high speed (drag and torsion loads). On larger aeroplanes, it may also be based upon flutter onset speed but microlight/VLA class aeroplanes rarely attract that level of analysis.
In flight test, the next speed determined is Vdf, the maximum speed found acceptable in flight test. There are many reasons for Vdf - it may be Vd itself, it may be a point (just below) where stability becomes unacceptably low, some flutter is encountered, the canopy starts to buckle inwards - anything that leaves the Test Pilot feeling that he's about to step over a cliff basically. On a few draggier aeroplanes (most flexwings for example) it's simply the fastest they could get.
Then Vne is normally set to 90% of Vdf; it's not allowed to be set any faster.
So in this case, I'd say its most likely (and I had nothing to do with either programme, so this is an intelligent guess) that something occurred on the microlight version testing to cause the TP(s) to set Vdf at a slightly lower speed than on the group A version. What that was, I've not a clue.
There is also a minimum safety margin between Vh (maximum level flight speed) and Vd. The margin is greater for microlight than VLA-category aeroplanes, which is probably the reason why things have been tweaked to give a lower Vh on the microlight version.
G