soj scales with different attack speed builds?
SoJ adds to the black damage portion of the weapon, so you could say it is a buff to the character sheet, before skill damage per hit or per tick is calculated. APS helps you to hit or tick faster.
one had 1.09 as and the other had 2.07 but both had just about the same sheet dps
Since they have the same sheet DPS, they will output the same DPS in-game, unless your skill is a channel or DoT type. Poison darts, for example, will give you the same damage output.
On the other hand, CoB identifies which APS bracket you're in:
1.09 is 2.22 ticks per sec
2.07 is 4.29 ticks per sec
1 tick is half a "hit". Depending on your "damage per hit", the 2 different APS brackets may give you different results.