R – sIFR3 – renders beautifully but links are not clickable

The Flash movie seems to be corrupted. Opening it in a browser should display 'Rendered with sIFR r436', but it's blank.

sIFR can only replace what is both in the document at the time of replacement, and displayed on the page. So in your case, indeed after loading the new content into the page, you must do the replacements again.

I've noticed a few animations, it's possible the timing is incorrect, meaning that the content isn't actually displayed yet when you do the replacement.

Not sure what you mean by not being able to load new text if sIFR replaces the placeholder text, but it sounds like sIFR might be preventing the code responsible for loading text from firing. This could be solved by hooking up an event manually, using the onRelease callback you can specify in sIFR.replace().