Give the guitarist options. Ask "is it, like, quieter or something?" or, "does it sound out of tune", "does it sound like you're in a different room when I play that note?". I do a fair amount of live sound and recording, and you'd be suprised how many people can't describe what they're hearing, but when you ask a simple question like "does it sound quieter?" they are for some reason able to think again and say yes.
Resonance is a funny thing. You could have something, somewhere, resonating with that note. I've found on many occasions a certain note on a certain fret will cause something in the room to resonate (or more annoyingly, in the amp/speaker). But if I play the same note in a different position it will be fine. The particular fraquency content of that one note in that one position is what's doing it. This could explain why it doesn't happen with a pick. The sound created when using the pick will have drastically different harmonic content. All this could cause something to vibrate, or cause comb filtering with some other instrument or even with the ventalation system around you. You may not hear the vent, but it can interfer with your notes. You could have a duct nearby pumping out a very quiet C plus 10 cents or so. If you play in tune officially, it will beat and make you sound out of tune.
Here's my advice:
Try everything. Play by yourself, play with just you and the guitarist. Add or subtract the other instruments. Play the note in a different position. Pluck every possible way you can think of with your finger. Is your nail hitting? Change where you are in the room. Change where he is in the room. Change the room. Change bass, cable, amp, speaker, etc. Record it and see if it's there on playback. Has the guitarist said anything yet? Is he awake?
If nothing else works, give him a bass to hold and maybe then he'll be smart enough to tell you what the problem is. We are bashing guitarists, right?