Since these shortcuts do highlight the corresponding palette entry, I would not expect a great difference.
The tests I would recommend:
Use "nudge up/down" to raise or lower the pitch by halfsteps; if this makes the the accidentals to display, the problem would be in the pencil entry system. Else, it would be more internally.
Listen to the entered tune, particularly to the sequence of a given note, followed by that note with a (failed) accidental. If the tune changes, it would be a kind of "hidden accidental" (I have one in a specific situation, I'll write soon about it).
I don't remember if there would be a means to show accidentals in another color as the notes (and to have the accidentals accidentally shown as white).
André Baeck, (Belgian, now living in the south of France); also known as Andre_B
User of Encore 5 since March 2009 - Windows 7 (and XP)