I am running a dynamic schedule that creates and emails reports for about 600 different people. My problem is that somewhere during its processing it will revert back to where it started and begin generating the same reports and sending them out again. My table is sorted by email address. The schedule may generate and email reports from the a's to the f's but then will revert back to the a's and start sending out the same reports again. Never had a problem on v4.5 . This started when I went to v5 .
I am running 700 reports on a similar setup to yours on CRD 5.5 with no problems so I don't think the new version is the cause.
However I do remember that when I migrated from 4.5 I had some issues with two of the schedules the migration wizard pulled accross. One was dynamic. When I re-wrote both schedules in 5 the errors wet away.