I am still having the same issue with Ubuntu 13.10, Gnome Desktop and Dia 0.97.2. I have fixed it by editing the start script /usr/bin/dia to have the LIBOVERLAY_SCROLLBAR=0 before the dia launch. /usr/bin/dia is now as follows:
#!/bin/sh
#
# Wrapped that calls dia in integrated version
#
I am still having the same issue with Ubuntu 13.10, Gnome Desktop and Dia 0.97.2. I have fixed it by editing the start script /usr/bin/dia to have the LIBOVERLAY_ SCROLLBAR= 0 before the dia launch. /usr/bin/dia is now as follows:
#!/bin/sh
#
# Wrapped that calls dia in integrated version
#
LIBOVERLAY_ SCROLLBAR= 0 dia-normal --integrated "$@"
This fixes the issue with the comment boxes as far as I can tell and still allows launching by calling dia from Alt+F2 or terminal.