Hello,
I realize that I am new here, and this is an old thread. But, if you are still working on issues with this, perhaps we may be able to help each other. I'm migrating a product from using a Vinculum-1 to a Vinculum-2 (we only use the Vinculum chips as USB Host controllers and for FAT support so we can do automated firmware upgrades from flash drives on our industrial controller). I am also encountering some issues which seem to be related to thread execution and/or blocking behavior pertaining to the "invisible" and thinly documented functions of the Vinculum-2 OS.
While I have not seen the exact occurrence which the OP inquires about above, I have observed what I can basically say is a complete ignoring of FIFO/comms/command services while the Vinculum-2 is apparently engaged in trying to enumerate, connect and load the FAT table from various drives. I am working on ways to try to mitigate the impact of these on the host communications side, and also try to find a way to have better visibility into some of the FAT related system, to deal with mysterious issues with file command processing.