We have a confirmed bugreport about this exact configuration from a German customer as well, and the current state is that he wants to try setting the Kick3.0 jumper (for $c0-mem reservation) in order to keep Kickstart memory from being added to the freemem list.
Your report here now confirms that this is a valid workaround until we can reproduce and fix the bug here. Trouble is that the programmer who did the new version of ACAtune is the same guy who is currently busy making the config/flash tool for Indivision AGA MK2.
In other words: Please understand that it'll take a few weeks until we can turn to this one. Since it's not a showstopper at all, the workaround should do it for you.