Thanks for the advice. I uninstalled 5.0 and installed the pre-release (6.0.1035) instead, but I'm sorry to say that the instability came right back.
You can download a trial version of AutoPano Giga från Kolor's site if you want to try to reproduce this error yourself. Just make sure to replicate my environment as closely as possible, i.e. AutoPano Giga 2.5.0 x64 on Windows 7 SP1 x64 with more than 4GB RAM. Especially the >4GB RAM part since I don't have any problems on a PC with only 4GB RAM.
Regards,
Stefan