I am experiencing the same issue, It did delete the log files once and then never again. If you have come up with a solution, any help would be appreciated.
First off, make sure you have the Remote Agent installed on the Exchange server, and Exchange 2k System Tools installed on the backup server. The backup method under the General tab should be set as a FULL (NOT a Diff or Incremental!). In addition, the Exchange tab should have "Full - Database and Logs (flush committed) as well. If you try a Full Exchange backup on a Diff job, it may or may not work. For this reason, I suggest running a seperate job for the Exchange servers if, for example, your policy is to run Diffs on weeknights.
Another thing to watch out for is to backup *just* the store (which actually backs up and flushes the logs as well) and not both the log directories and the store. Running a backup of e:\logs\*.log will not flush anything.
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