Invisible skill penalties

[Avastgard]

I started a playthrough using Skytweak to alter Skill Level Cost Power, which is supposed to make all skills (and, consequently, the overall player level) level up slower. Vanilla is 1.95; I had it set to 2.5. I also edited the Elys uncapper .ini file to give me more perk points on level up (3 up to level 10; 2 up to 20, etc.).

Everything was going great and I really was leveling up much slower. When I had almost 23 hours of gameplay I was still on level 10. But then, for some reason, I noticed that many of my skills were dramatically reduced. There were several invisible -15 penalties being applied to some skills, even though the skill levels were not shown in red. The skills affected were all the thief skills plus Illusion, Conjuration, Destruction and Alteration.

The weirdest thing is that using the console commad "player.setav <skillname> X" did not work unless you would set it to a higher number than the penalty. So, for example, Conjuration was at 0 when it was supposed to be at 15. Typing "player.setav Conjuration 15" did not do anything, but "player.setav conjuration 30" would set it to 15. So there is a persistent -15 penalty being applied. No idea what caused it, though. Perhaps one of the diseases from iNeed got stuck even after curing it. The Active Effects screen is indicating no penalties or any negative statuses whatsoever. None of the skill numerals were/are red.

I noticed this shortly after reaching level 10. Searching through my save files, I found out that this penalty showed up during the Proving Honor quest. The autosave right when I enter the word wall room in dustman's cairn (where Wuuthrad is) had all the correct skill values, but a hardsave I made with Autosave Manager during the battle against the draugr a few minutes later was already suffering from those penalties.

What could cause this invisible penalty to keep being applied persistently? Any ideas on why this might have happened and if it's OK to just use the console to fix it?

[Avastgard]

Yet another quirk: after using the console commands to attempt at fixing the values, the skills show up the correct value (the one that was supposed to be from the beginning, if nothing had gone wrong) on the skill menu. This same correct value is shown when using the player. getav command. However, if I enter the individual perk trees, the value show is 15 points higher than what getav tells me, and this counts towards perk buying (i.e., this new +15 value is the one used to check if I have the necessary skill level to buy a perk). Also, when reading a skill book, it told me my skill had increased to the +15 level.

So, apparently, I now have two different skill values: one for the actual Actor Value and one for the perk buying tree interface (+15). This all leads me to believe I do have an invisible penalty on my character that was supposed to disappear but didn't. And when I used console commands to "restore" the AV's to the correct value, I actually created an offset on these skills. The mystery grows...