Edit: I think I have figured out what is going on. I think it is a result of the improved/soft prestige, so it is immediately going to progress on the previous layer that those upgrades are listing. Since my level/floor/multiplier is so low compared to the values needed for that layer, it takes a significant number of short runs to get back to the point where the DISPLAYED layer is really upgrading, which is why once I get high enough to really affect that layer it starts increasing at the expected rate once again. I have had a couple times recently where I prestige to a new layer for that ascension (this time was 25) and when I get back to the previous layer my point gain for that layer is... negligable. I just went from level ee8 to ee14 (similar floor gain, multiple orders of magnitude) to go from 1 point layer 24, to 30 points layer 24. I do not gain any extra progress from getting higher levels/floors during this period, it is the same 2-3% progress per floor change regardless of which floor it is on. i.e. if my current max floor is 3.2e10 I will get 2% point progression from going from floor 1.0e10 to 1.5e10 as I do going from 3.2e10 to 3.4e10. Normally, the higher level/floor would cause significantly greater progress, but while this is occuring it does not. At around 30-40 points in that layer it speeds up suddenly and I go from 3-4% progress regardless of floor, to 0 progress on previously cleared floors, but 50% to 400% progress for each step on 'new' floors. Once I get back to the layer I last prestiged on, it continues acting as normal, so I only need to multiply my floor by ~10 to get to a new layer again. For this example, I hit layer 24 with a layer 1 multiplier around ee8, and my layer 1 multiplier was around ee12 before I got point 30 in layer 24. I hit layer 26 with a multiplier of ee14. So I needed my layer one muliplier power to increase by 4 orders of magnitude to get 30 points in layer 24, but I got the rest of 24, and all of 25 with only an increase of 2 orders of magnitude in my layer 1 power. Anyone have any clue what is causing this?

Your conclusions are pretty much correct. You might be progressing at layer 1 but because of improved soft prestige youre getting points for the highest levels (extremely slowly) so the game show the progress of the highest layer of points youve gained during this run. So the display of progress is misleading.