Just a FYI you still haven't fixed this, even though it's in the Old Bugs section.
One way of stopping it would be having it only grant you the extra stuff after you've died at least once since last spawn. Your very first spawn wouldn't give you anything, but seeing how it's your first spawn, you'd only have 0 skulls anyway.
One global boolean set true in player_death, and the "bonus" you get would be encapsulated in a simple
if( bool)
{
//Bonus here
bool = false;
}
from what i can gather, it's giving you the bonuses if you sit in spawn and change classes?
why not simply make it so that you lose all skulls when you suicide (from non-environmental dmg) and when you change class?