My Mark IV won't sustain on a specific note

[wastoid]

Have you tried it with another guitar? Or have you tried that guitar with another amp recently enough to remember accurately?

Sounds like it could be a pretty classic dead spot issue on the guitar, not the amp.

To add to that a little bit, try this: Turn on your setup and play like normal and observe your Es dying prematurely. Then pressthe tip of your headstock against a nearby object (like a table edge) and see if the problem goes away.