Thanks for the reference to the work item as it made it more clear to me why you're likely still experiencing this issue.
The original problem was that pasting images into documents resulted in inline binary image data being directly injected into the source of your artifact. Such content is not supported by the publishing engine. The fix you referenced was to ensure that, going forward, pasting an image into a document would first upload that image as it's own (uploaded data) artifact and then inserting a reference to that artifact into your document.
The issue for you is that this doesn't do anything for pre-existing embedded image data. There are a couple of options:

1. Extract the image from your document and re-paste it using 4.0.1 so that it creates the image resource and adds the reference to it (or extract it to a file, upload it to the server and add the reference yourself).
2. Contact IBM Support. We have a utility which will scan your repository for embedded image data, extracts it to a resource and replaces it with a reference to the new image resource in your document. This has the advantage of finding all such occurrences currently on your server.
   Here is the link for contacting Support: http://www-01.ibm.com/software/rational/support/contact.html . Ask for the FixEmbeddedBinaryImageLinks utility and they will be happy to guide you through it's usage.