You could try checking bpdbjobs every so often from cron, and keep track of the job ID numbers. Yes, it's a pain but I've worked with customers that have done this.
With 6 you should not have as much of a problem with it as the scheduler has been re-written... that being said, it's still possible, just less likely. The problems in 4.5 and 5.x usually stemmed from either a lot of media servers, network issues, a really busy master etc... bpsched stuffs a bunch of requests into a message queue, and then reads them out of the other side. If the master is busy, or bpsched is waiting on hearing back from a media server (by checking in with bptm), then it has to process those requests sequentially from the message queue. bpsched is a single-threaded application, and one of the ways around it in the past was to get a faster master server (or faster processor for the master)... or change the configuration so that the master wasn't as busy. Keep in mind that the master might have to service a lot of vmd requests as well, which can become very significant as the number of media servers increases.
Brian