It was a very odd thing and was easily fixed by changing to selectOptions which is what I needed instead of checkboxes anyway. I am hoping that I had some sort of error in my code that caused the issue, I am sure that others have used selectCheckboxes just fine before.
My guess is that some sort of syntactical error that Eclipse didn't catch is what caused the issue, however since it is gone now I do not plan on digging further into the matter.