The flag in filetypes.conf 'comment_use_indent=true' is ignored. Comments that are not aligned to zero are treated as text.
built on or after Aug 18 2009
I just tested it with ~/.config/geany/filedefs/filetypes.c and it works as expected. What filetype did you try?
Some example code with steps to reproduce would be helpful.
Seems to work on Geany 1.23 (git >= c05f1bd). Closed due to no further information provided by OP.