I don't really understand it. Along with a billion other things in the game.

I left my manual back in my home country!

Can someone explain this penalty? All i know is that it gets higher the heavier armour you wear...

There's a .pdf version of the manual(s) in your /nwn/docs folder for reference.

The penalty represents heavier armour being more restrictive, which is generally but not always the case. The Skill Armor Check Penalty is basically the amount of skillpoints you need to add to some of your dexterity-based skills (it's a negative number).
Other restrictions are represented by capping your dexterity at lower values for heavier armour, which amplifies the above effect and also lowers your AC bonus and reflexes, and giving the armor more weight (possibly reducing movement speed).