So I just installed Fallout and the main mods suggested in the sticky thread to fix up bugs and get a better resolution. But when I was making my character I noticed that some of the skill values were wrong. For example Small Guns says it should be 35+AG = 40 for a unmodified character which is what the skill shows. But for example science says it should be 25 +2*IN = 35 for a base character, but the skill says it's actually 55 for a default character. I don't want to start my first playthrough with an overpowered character, so does anyone know what's going on and how to fix it?

If you tag a skill you get 20 extra skillpoints at the start.

You also need to factor in Traits: Skilled raises all your skills, while Gifted reduces them (the latter is severely overpowered, as free 7 SPECIAL points are not to be frowned upon, even at the cost of lower skills).

Also check your 'Game Difficulty' setting. It affects skills a lot.