This is a nasty SharePoint bug which caused some trouble in one of the SharePoint Online environments I was working on.
I created a Site Template using the “Save site as template” feature of SharePoint. Now when I created a new site from the template it resulted in the web parts all mixed up in the Left web part zone. Remarkably it was only the Left zone, the others were keeping their correct web part sequence.
When I took a look in the Onet.xml of the Site Template the web parts were nicely divided into seperate AllUsersWebPart’s and having correct WebPartZoneId’s. And although the web parts were also mixed up in the XML, the WebPartOrder properties were set correctly, 1 for the first, 2 for the second and so on. I still tried to rearrange the XML so the web parts would also have the right sequence in the syntax, but with no success, the web parts were still mixed up.
The final thing to do was to create a Web Part Zone for each Web Part. I did this by opening the page in SharePoint Designer and edit in the Advanced Mode (button on the ribbon).
This way the order is hardcoded on the page. I admit, it’s not very neat, but it does the trick.