Junctions (etc.) should work in Opus 9 but maybe something's going wrong due to this combination of junctions and Truecrypt containers.
I'll see if I can reproduce the problem here.
When you mount the Truecrypt container which settings do you use:
Read-only?
Removable?
NTFS or FAT format?
You might also be able to unearth some useful information by following the debug steps in this FAQ:
[Changes to folders are not being detected)
Let us know what you find and I'll try to take a look at this on my machine as well.