"Failed to use non CLS compliant type" when iterating SPLimitedWebPartManager.WebParts

I haven't been able to get passed this while using the web part manager, so instead I used the SharePoint web part pages web service, using this article from Raymond Mitchell as a reference:

Update a SharePoint 2010 Web Part from PowerShell

The web service returns all the web parts as an XML string, which can be converted to an XML Document, and I was then able to update the nodes I needed.