Unfortunately, I only know the workaround on a Mac, but it might help as long as you can track the directories and might help Mac users who have suffered the same fate.
For whatever reason, AME is placing the presets in a new location without Prelude knowing about it. Ill communication. Basically, Prelude is looking in one place for the presets and the new Media Encoder is placing them elsewhere.
The workaround is to find where AME is placing them and move them to where Prelude is looking for them.
On a Mac, the solution is to take the presets User-- Documents--Adobe-Adobe Media Encoder--8.0--Presets and move them to where Prelude has always looked for them and where AME always previously stored them. User--Library--Preferences--Adobe--Common--AME--8.0. On some machines, Adobe created an alias inside of here to point to the Documents folder and that solved it, but for whatever reason, it's inconsistent.