This is now fixed and will be available in the next release v2.0.1.
There was a problem in the hashmap which stores a list of folders in the system. The map was incomplete and because of this, returning a null for certain folder lookups. I've tested in a system upwards of 5000 folders and its working fine now.
For reference, the check-in was logged under: BITBITOOL-651. The ticket referenced above in a previous post (BITBITOOL-750) was a duplicate.