David,
I've seen the same problem, well very similar. Since the only plugin I'm using that touched .htaccess is this one and when I disable it and edit the file, then reactivate it and the problem returns, I don't know what else it could be.
My file doesn't have partial words like yours, it just has many instances of the permalink rewrite - the whole thing - and then multiples of just #BEGIN WORDPRESS #END WORDPRESS.
Do you have anything else in your .htaccess file? I have a customized file which includes stuff for caching, security, and optimization. I'm trying to drill down here to see if it is an interaction with the coding I've put in or if it is just going to happen anyway.
Thanks