When exporting a workspace in Confluence, all the Info, Tip, Note, and Warning macros we put in did not render properly. Therefore, the boxes and the icons did not show up correctly in the PDF.
What version of Confluence are you running? There is a closed ticket with this exact problem which Atlassian have fixed from Confluence version 6.13.0 and 6.14.2 and up.
Here is the link to the closed ticket for reference - https://jira.atlassian.com/browse/CONFSERVER-31307
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