Geany invisible underscore
Solution 1:
Same issue, Ubuntu 20.04
The problem is well described here:
https://github.com/geany/geany/issues/1387#issuecomment-287537022
Some fonts write underscores below descenders but don't include that in the declared font height, this is technically incorrect and confuses the layout software in Scintilla (the editing widget Geany uses) so insufficient height is allowed for underscores.
The solution is to either change font or to instruct Geany to make line height bigger:
Tools > Configuration Files > filetypes.common
[styling]
line_height=0;2;
Solution 2:
It turned out that the problem was with the Monospace font. This happens also with other programs, such as LeafPad if they use that font.
The solution was to change the font to something else - "Lucida Console" in my case.
Edit: It seems that changing the zoom fixes it, too. Some zoom levels have invisible underscores, some don't.
Solution 3:
For future reference, I had the same issue with Monospace 14 in Kubuntu 16.04, and it was solved by installing the recommended nvidia driver for my graphic card.
Edit: Despite the anonymous downvoter, this solution worked for me and I discovered it by chance. It means that it is a display problem. I didn't find any reference to this with search engines, so I'm pretty sure it can help someone to find it here.
Solution 4:
Sorry for the very late answer, but this problem still persists.
For me, this was fixed by changing the font-hinting setting from 'slight' to 'medium', which looks like a bug to me.
I am using Cinnamon but I guess this would also work in other desktop managers.
Solution 5:
A followup to Gael's answer which does the trick BUT
you must uncomment "[styling]" for the new line-height directive to take.