Sort of resurrecting a dead thread here. But this is how I started to find my solution, so I'll report it here.
I have the 'nalia/aerie stutter' problem as described above. Basically it appears to happen because the global variables are stored in a hash-map which doesn't dynamically resize as it should when it gets big, as described here:
http://forum.baldurs...-stuttering-lag
This is probably why starting a ToB game works - ToB must either reduce the load factor at which resizing occurs or change the initial bucket size for the engine's hash-map implementation. The problem is likely worse if you have TDD or CtB installed because those mods have many global variables. CTRL-Y Nalia works because many scripting blocks apparently have an early variable check if there is "mage/thief" character or similar - see this discussion:
http://www.shsforums...the-stuttering/
The problem almost never happens anymore because people use ToBEx which implements a bug-fix for this. I was having weird sound-problems with ToBEx that I haven't worked out, so I still was running into the problem.
Anyway, the solution proposed here:
http://www.shsforums...the-stuttering/
(create a bunch of dummy global variables enough to finally trigger the dynamic resizing of the hash-map) worked fine by me. I used NearInfinity and copy pasted the proposed script in.