As of 10/08/08, MOTU is aware of the issue, and will fix it in a further update.
As a work around, you could Freeze the track, then do the bounce to disk, as was the practice in versions before DP6.
(example is for MachFive2)
Go to Macintosh HD/Library/Audio/Plugins/Components and be sure you’ve installed the AU version of MachFive2. If it’s not in there, install it from the disk and do the latest update.
If it’s in the Components folder, go to the MAS folder at that same location, and put the MachFive2 MAS.bundle in the trash (or stick it somewhere you can retrieve it if necessary)
This will cause DP to not load the native MAS version and use the AU version, which they say DOES work correctly.