First, have you read the How To topic on Change The Invoice Number Starting Point? It’s a bit complicated but then again so is the logic SI uses to determine the value. In the simplest case, there is only one index record and all preferences get their numbers from that record.
For me to try and determine what is happening on your system, I would need you to export the si_index, si_invoices and si_preferences tables. Zip them and attach the zip file to a response to this message. There is no revealing data in these tables as identities exist as numbers to the ids of records in other tables. You can review this to verify it to your satisfaction before giving me the data.
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