Hi! a user of the french forum reports an issue of an "unknown error" and encoding failure when he encodes a sequence with a dynamic link is used, and AE is running, while the encoding works if the sequence is rendered from disk and AE is not running.
For more info: http://forums.adobe.com/thread/1108045?tstart=0
Unknown Errors are tough because their cause is 'unknown', and without a defined case we have no defined solution.
If he has a method that does work, just use that.