I haven't noticed this myself, perhaps. Can you provide steps to reproduce it? What version of Geany are you using?
I'm afraid it seems a bit random (Geany v0.15 / r3012 on Ubuntu 8.04 - same with v0.14 before though). So if nobody else has noticed this issue, don't worry about it for now - I'll report back here as soon as I can make out a reproducible pattern.