Well, I only have two power buses and one is dedicated to the IR LED circuit and the other is dedicated to the detection circuit. And the only difference between them is that each uses a different ground.
Are the two grounds electrically the same?
Not sure about the two power buses, are they from a different source?
Either way, as I said, that simply can't happen if it is wired as described. Think about it, all that you are doing is adding a capacitor across the supply, this can't affect the signal. What were you seeing that made you think there was a delay.
different types of capacitors had different charge/discharge rates.
Well I would not say they are different charge/discharge rates but the capacitive reactance and effective series resistance are different with different types of capacitors.