It might be worth trying the debug stuff in this FAQ but I'm guessing that subst drives are like NTFS junction points to Opus: The system will be reporting changes to the real path and Opus doesn't know they apply to the path it's looking at as well.
I'm guessing you need to use the subst drives for another program and you're not using them purely as an organisational shortcut. Opus aliases are not visible to other programs but they may provide an alternative to subst drives if you're only using them as shortcuts for file management.