I've now tried changing the resolution to 90dpi
I think that's probably a typo, but since it's so important (for other readers) the dpi for version 0.92, is 96.
I don't have a complete understanding of the viewbox. The understanding I do have, is that the viewbox tells browsers how much space is needed to display the image. It may have other consquences that I haven't learned about yet. But my best understanding at this time, is that it shouldn't be affecting those extensions.
However, the change in resolution could have (as far as I understand). If I had the proper formula (or could figure out what it should be), I would calculate whether the 6 point change in resolution would cause exactly and precisely that result in the change of orientation points. But I'm generally somewhat confused about dpi. But that might be a clue, if you understand enough to do the math.
Are you having this problem with a drawing you made using an older Inkscape version? Or does this problem affect new drawings? If it's affecting new drawings, then the problem is nothing to do with the viewbox. (Because the viewbox is new for 0.92.)
My best idea about this, is that the extensions need to be updated. I don't know exactly why, if it's because of the change of dpi or something else. But lately, a lot of extension have needed updating, for one reason or another.
I would suggest...well, a few things, one of which I'd be glad to help. Ask on either the development or user's IRC channel about this. Ask on the mailing list. And if those native gcodetools you mention are the ones made by the Russian guy (or team, I'm not sure), then post in that English thread on the Russian forum about it. All those extensions contain the address of that thread.
For me, it's frustrating to visit that thread, because it's a single topic, with over 40 pages, the last time I looked. I don't know why he didn't make a whole board, because that would make it easier for people to search for the info they need. Maybe didn't realize how popular those extensions would be. But as a last resort, and if he's the author of those extensions, then I would certainly visit and post.
(I really should try to remember his name, so I don't keep calling him "that Russian guy". I'll start now..... Oh yes, it is a team. See Extensions menu > Gcodetools > About > Help tab. But the lead developer, and who runs that forum, is Nick Drobchenko.)
The part I could help with, is to post to the mailing list, and convey any response we might get, in case you didn't want to subscribe (I think you have to subscribe to be able to post to it).
BUT, if the extension you mentioned first carries a non-free license, (whether you pay for the extension of not) then it's not going to help for Nick or his team to fix the gcodetools extension. At the same time you ask Nick and/or the Inkscape developers for help, I would contact the author of that extension as well. If it carries a free license, then anyone could fix it, and you would need to find someone who is willing to fix it.
Hhhmm....well, not unless that jtechphonics extension actually calls up and uses the Orientation Points extension. If the part that needs fixing is ONLY in that extension, then yes, getting it fixed should fix the problem. But I really have no idea how it works.