Phoebus, not sure if this helps or not, but I manually upgraded vanilla 34.04 (linux) to Phoebus 34.04v02 (linux) using the steps below, and still get the intermittently missing text. I didn't try the Vanilla build before hand, so i don't know if the problem exists there or not. My world was 250 years, default (non-advanced) world gen except I changed metals to "frequent".
My linux vanilla-to-phoebus steps are:cd ~/Games/DwarfFortress
rm Win32Ph/raw/graphics/graphics_example.txt
rm -rf Win32Ph/raw/graphics/example
cp -R Win32Ph/raw/* Phoebus/raw/
cp Win32Ph/data/art/* Phoebus/data/art/
cp Win32Ph/data/init/colors.txt Phoebus/data/init/
cp Win32Ph/data/init/init.txt Phoebus/data/init/
cp Win32Ph/data/init/d_init.txt Phoebus/data/init/
cp Win32Ph/data/init/embark_profiles.txt Phoebus/data/init/
cp Win32Ph/data/init/embark_profiles.txt Phoebus/data/init/Win32Ph is the Windows version of 34.04v02,
Phoebus started as a copy of Vanilla 34.04 for linux.
Based on what I'm seeing, I believe the problem is with the TTF code, not your tileset. I'm not sure of this, however.
For the person that was asking about a Mac version of the Phoebus tileset, the steps above should work for you as well -- get the vanilla version of
34.04 34.05 for Mac, grab the Windows version of the Phoebus set (with a matching version), and make the changes. All this changes are the raws, graphics and config files, not the executable. You will, of course, need to adjust the commands for the directory path you are using. I have the versions side by side in my Games/DwarfFortress directory, and made sym-links with the above names to better track which one I was in.