So first I spent 30 minutes trouble shooting why the sustain pedal wasn't recording along with the keyboard (seriously, I need a two step workaround to accomplish this?)
Now I finally have the data recorded but the sustain is not acting as it should. The sustain only works on notes that start after the pedal is depressed, but notes that are being played and held while the pedal is engaged get left behind, effectively cutting them off as soon as the note is dropped. I own Pro Tools, Logic, Cubase...none of them behave like this and all are using the same configuration. Apologies if I'm being dramatic but this doesn't seem like something that I should have to worry about in 2016.
video link so you can see/hear the problem:
https://dl.dropboxusercontent.com/u/20123254/File%20Aug%2010%2C%2010%2028%2021%20AM.mov
MacBook Pro Retina
2.8 Ghz Intel Core i7
OSX 10.11.6
S1 3.2.3
