Certainly not! I go back and forth between two fonts depending on my mood. One is a sans-serif, the other is created from actual pressings from an Underwood typewriter! Since I actually still do a lot of writing on an Olivetti (another mood thing), it is nice to see a familiar stroke in both mediums. So, I would be the last one to score a strike against anyone who prefers Courier 12pt, being a young digital tyrant notwithstanding!
But anyway, I have reproduced your error! At first I thought you meant the underscore was diminished, but from further posting I see you truly meant invisible, and indeed that is what I see. Underscore in the regular editor—completely invisible in full screen.
Screen resolution, font magnification, all of the usual suspects have absolutely nothing to do with it!
The problem is clearly that the underscore is being drawn in black, while the text is being drawn in orange. This can be confirmed by selecting a block of text and noting that the underscores are in fact there, but black against the now lighter selection colour.
This is especially odd that others are not able to reproduce it. Some setting or potentially a bug is causing this to only happen some of the time. I cannot find the source. I tried changing the colour of the underline manually using the font palette, I changed it to bright red, and then went back into full screen. The underscore stayed bright red.
So I selected a range of text that includes underscores, and using the colour palette, change the colour of the text. The underscores stay black for me, which would make sense. But! It gets even more fun.
Making a new underscore in the coloured area produces a matching underscore—not a black one! This particular underscore will respond to Full Screen’s edicts of orange-ness! Not only that, it will re-colour to black. But that does not guarantee that it always will. A convert to default editor settings command to reset everything causes the error to revert (though note, this does not reproduce the error reliably in documents that do not already exhibit it).
Yes, because further down the Rabbit Hole, newly created documents do not exhibit this. But newly duplicated documents from older documents I have not edited in a while, do. In other words, I can reproduce this error in some documents but not others, within the same project.
It should also be noted that this does not appear to be related to Courier at all. I can reproduce it using several different fonts chosen at random.
Incidentally, this is the latest Scrivener beta, running on Tiger.