I just ran into the same problem Mary B. reports. HOWEVER, I have three levels of the site and on my production site, I do not see warnings about the deprecated function use. However, on my test site I get those deprecated errors. I have not run or installed the plugin on my dev site.
Both sites are using WP 3.1.3, but the prod site is using a theme I cribbed from the WP free themes section and my test site is a theme I am coding up mostly from scratch (but not quite 100% from scratch). I've been using your plugin on the Prod site for sometime and have been keeping it up to date. I just (within an hour of this post) installed the plugin on the test site.
I saw the note about no broken functionality and the message WP throws is identical (except for paths & site specific items) to what Mary B. Reports.