Ari Gold,
Distances OK
Stops and transits OK
I certainly can't see any breach of the OW rules in what you are trying to do.
My guess is that you will find your answer (or at least your explanation) in Married Segment Control. In this case maybe you are being blocked from booking 2 connecting flights with the one carrier.
I am assuming (a) that you know awards are available for all flights and (b) you're trying for a J award, so if that's the case, the possibilities I'd investigate are:
HND - HEL - BRU (if your're trying to book both flights with AY).
HEL - HND - SYD (if you're trying to book JL for both flights, which you almost certainly are, given that your only alternative to JL is AY, which I know from my own recent experience has been showing zero availability for HEL - HND).
The third possibility (least likely because of the lack of AY J awards from HEL - HND), I see is AMS - HEL - HND if you're trying for AY for both flights
I'd experiment a bit to explore these possibilities:
Change the dates for the HND - HEL - BRU flights a little to make HEL a stopover and see if that fixes your problem. Keep all other particulars the same, particularly the carrier.
If that doesn't work, I'd do the same for the HEL - HND - SYD flights by including a stop in Tokyo (you will need to temporarily change your original stop in HND to a transit to try this)
MSC can be a very confusing animal to try and make sense of, especially because the same airline may only apply it to some individual routes, and not others. I recently booked JL for LHR - HND - SYD and it got ticketed without problems but that was after I couldn't get HEL - HND - SYD with JL to work. Same airline, different result.
Your fix could be as simple as converting one of your transits into a stopover in one of these cities (in my case I was hamstrung by the fact I had already used up all my 5 stopovers)
Good luck