Avogadro 1.2.0 sometimes wann’t show certain labels. Sometimes it does, sometimes - not. Sometimes it is “0”, sometimes “2”. For example: https://yadi.sk/d/qpZmSLJ53GpqPD
I’m happy to revisit bugs, particularly if we can reproduce and debug them.
In general, labels are hidden if the algorithm decides the atom is too far from the camera point.
I’m a bit surprised by this particular image, since “0” should, in principle, the same distance as “3”.
Can you post the file? (i.e., as text, not image)
There is some difficulties to post non picture file, does link is available?
https://yadi.sk/d/KzMhqCIU3KFBC4
I can reproduce this on Avogadro 1.1.1.
Huh. Now that’s a weird one.
I’ll check it out, but is the problem systematically with the custom labels?
I can’t see any system order. Unvisible lables are differ from time to time. Very very rare it’s everething ok. Sometimes labels become visible if changed to another latter, sometimes not. Sometimes they appear while opening at the flash moment and became just pale footprint on a shadow
The error moment
Any another file during this session is without “1” 
I found a way for correct lables. Firstly is needed to use draw tool and only after that file would be opened
