If you are sure that no one is doing anything in ACCPAC Plus Order Entry, then run an Adagio Data Integrity check and make sure your data is clean.

Adagio needs to know the number of orders, invoices and credit notes on file and so keeps an internal count. Every so often it checks its internal count of the sum of the documents against he number of documents in the file. If the counts don't match, Adagio OrderEntry goes and counts the specific number of each document type (since that means that something external has added or deleted an order, invoice or credit note).

Finally, what version of OrderEntry are you running? (See Help | About).