There’s an annoying bug in Quotes module, in that the line items don’t retain the order in which you add them to the quote, and also every time you edit and save they get rearranged again.
Using v7.2.0
For completeness, this issue was finally fixed here:
73772 : The quote's line items may not display in the same order as it was added after saving the record.
http://support.sugarcrm.com/Documentation/Sugar_Versions/7.6/Pro/Sugar_7.6.2.0_Release_Notes/
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CRM Business Consultant