This sums up the issue:
I have a custom part which has it's own post backs. The problem is when I am editing, a post back from the part is called and I get an alert (To save your changes before continuing, click "OK". To continue without saving changes, click "Cancel".)
I noticed that for me the alert goes away when I deactivate the "SharePoint Server Publishing" feature on the site. Unfortunately for me I need the Publushing feature active so I still need a workaround.
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