Why do I continue to get the "Align 20 Hz to 3.6 GHz Required" message even though I ran the Align Now, All routine on my MXE?

Although the alignment that you ran is called "All" it still does not run all of the instrument alignments in the MXE. There are also RF Preselector alignments that need to be run on a periodic basis. These can be found under the System, Alignments, More, RF Preselector, Align Now menu.