I reconnected everything up and used the oscillscope to measure the signal coming out of the H-Bridge.

The measured output looks a lot like a square wave to me. Which means that the motor driver filters out noise and my SPWM signal is considered noise.
I measured it again using two 4.7k resistors in series as a load. Same thing.

Well I guess I learn new things everyday. This time I guess I really should have read the datasheet properly and understood the device.
Back to the drawing board for the h-bridge design. :)