This is my favorite quality mod for balancing and progression. But I ran into two problems.
1) Just an inconvenience. The mod displays upgrade chance for each researched tier where relevant. The problem is that this clutters the tooltip and pushes out useful information, especially later on. It would be nice to disable this, or have a toggle.
2) The actual bug. The upgrade odds from Normal to Normal+ are as expected = quality bonus. However, all further upgrades are listed as 4x the odds. Some testing suggests this is not just a visual bug and higher qualities actually do get this benefit (as opposed to vanilla where there is a hidden reduction instead).

Both things you reported have nothing to do with the mod (AFAIK).
Thats how base game shows this and actual numbers in the mod are not what in the tooltips.

1) Let me try to explain. The tooltip doesn't just say "quality: +10%" (for example), but under that it adds a list:
Normal -> Normal+: 10%
Normal+ -> Uncommon: 40%
Uncommon -> Uncommon+: 40%
etc for each unlocked quality.
I tested without any other mods, and all other mods I use without QualityPlus. This list only shows up when I have QualityPlus enabled.

2) I have tested it in sandbox (once again, QualityPlus by itself and other mods without it) and it does indeed use those numbers. The amount of items upgraded from Normal to Normal+ vs Uncommon to Uncommon+ with all else being equal was too different to just be random error.

EDIT:
Okay I had a peek at the code.
Toward the start of data.lua, you define "local nextProbability = 0.4". However you set it for every quality except normal. Which means normal uses the game default of 0.1. For whatever reason, this makes the game display all the values. Setting the field to 0.1 stops the tooltip from showing up. And also fixes the second problem of wrong odds (because the probability was set to 0.4 instead of 0.1 base).

Thanks - Thats a good catch.
I had no idea that tooltip was caused by mismatch on probabilities.