Any info in the FMS event log?
Maybe the schedule trigger got corrupted in the conversion process. Try deleting it and creating a new trigger.
I encountered a similar situation recently. In my case, it was a scheduled script on FMSA11 to process about 2000 records and send email as appropriate, all within a 30-min. window, every 30 min.. The process ran flawlessly when via FMP client but resulted in numerous "Can't send email errors" (1506) in the FMS log when scheduled to run by FMS. The problem was solved by using an email plugin (we use 360Works Email) instead.
I suspect what was happening was that every time the built-in SMTP function is run, it tries to establish a new connection to the mail server. If you have a lot of email to send within a short time-window, the email server may balk at having so many connection requests from the same IP. Switching to the email plugin allowed us to establish a single connection to the email server at the beginning of the process, through which all subsequent emails were sent. The single connection is closed at the end of the process.
Something similar may be happening in your case, and using an email plugin may provide a solution. Good luck.
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