there's a lot of things that can contribute to sustain. sadly, strats have never been known for their sustain. being a bolt on neck style of guitar the disconnection between the neck and the body disipates some of the resonance... you can check to see if its your guitar by unplugging it and playing a note and listening to see how long the note rings out. a noise supressor or noise gate setting could be the issue... in this case you would have the sensitivity set too high. also, your pedal probably has a compressor. try playing with that. compression can really enhance sustain by closing the dynamic gap between softly played notes and loud notes. with that you get a more consistant volume note that rings longer.