Wordpress posts missing unless using default URL structure

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I've got a Wordpress install running alongside Magento and they were previously integrated using the Fishpig extension. I've recently turned off Fishpig integration because I want to use a new theme for Wordpress.

The theme has installed fine but posts and categories appear as missing if the URL in Wordpress is set to display as anything other than the default. eg. /?cat=2 rather than /category/other.

Has anyone experienced this before and know a solution?

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