My first thought is always that it could be a rogue plugin, especially if the issue is in C14 as well as in C5.
Do you use the same plugins in the projects? Have you been running C5 in 32bit or 64 bit?.
You could try starting Cubase in safe mode with plugins disabled (Start Cubase in Safe mode / Temporarily disable preferences, but disable third party plugins instead of preferences. Although you could do that in a second step) and see whether you can reproduce the issue. Of course, you won’t have any third party plugins, so just do some other stuff and try to save and provoke the behaviour).
If disabling third party plugins helped, there’s the tedious problem of finding out which one is the culprit. If not, dunno.