This is going to be too late to do you any good on the smoke you were doing yesterday, but:
In my experience, the main problem with keeping the AMNPS going is lack of airflow.
The glowing pellets need to have good airflow at all times so they'll have plenty of oxygen to keep the cherry lit.
Here's what I do in my MES 40:
First, I get the MES preheating.
Next, I microwave the pellets several times in a row. I nuke them for 30 seconds. Then I stir them and let them "steam off" for a few minutes. Then I nuke again for 30 seconds, stir and let steam off, etc., etc. I do this four or five times.
Then I load up the AMNPS. I put the pellets in pretty deep. I want them to be piled deep enough that the burning face will "draw" well. That helps keep it lit. BUT, you do not want to let any pellets reach across over the tops of the separators and touch the adjacent row. I want there to be decent separation between any pellets in adjacent rows so the flame cannot jump across and cause a "short circuit" in the burn.
I then put the AMNPS in the smoker and let the smoker continue to preheat. I think this is an important step because the pellets get dried out even more by being the the smoker while it's preheating. I actually leave them in the smoker for a half an hour after the smoker says it's up to temperature. This really bakes the moisture out of the pellets well.
Now, I take the pellet loader completely out of the smoker. This opens up the air inlet as far as it can go.
I open the top vent as far as it will go.
(I actually do this next step before I even fire up the smoker, but I'm just mentioning it now because it goes along with the whole airflow part of the description). I open the chip tray slightly. I keep it about an inch open. In the version of MES40 that I have, this opens the air path even more.
Don't confuse the chip loader with the chip tray. I leave the loader completely out. I open the tray thingamajig, too, as if I was taking it out to dump the ash. Hopefully this description also applies to the model of MES you have.
I have some foil on the bottom tray, over at the left side, above where I put the AMNPS so that it keeps any drippings from being able to dribble onto the AMNPS. This is another key. You cannot let any drips fall into the AMNPS. If they're watery, they will put the fire out. If they're fatty, they'll cause a horrible smelling/tasting smoke. So you must have something over the AMNPS to make absolutely sure that nothing drips down into your pellets.
The AMNPS must be up off of the bottom of the smoker. I place it on the pair of rails that are to the left of the heater and chip tray area in my MES. This is perfect because it holds it up several inches above the bottom of the smoker. This allows great airflow up from the bottom. If the AMNPS just sits on the bottom of the smoker, that restricts the airflow.
If your smoker doesn't have those rails, I'd find some other small rack to prop the AMNPS up on to make sure lots of air can get in under it
I NEVER use the water tray. Any moisture will inhibit the burning of the pellets.
Dry and lots of airflow. These are the main keys to keep the pellets burning well. Since I started doing things this way, I've never had the pellets go out. If they're still burning at the end of a smoke, I have to wrap the AMNPS in foil to extinguish it.
I hope this does you some good on your next smoke!