Hmm... actually I have spent some time on the Google forum looking at Sitemap posts and it appears that not everyone has had a happy experience of using this service. There are some references to 'Sudden Site Death' brought about after submitting sitemaps to Google.
There is no indication that this is Google's fault, but I gather that the robots that crawl sites under the sitemap program are of the 'smart' variety. They are smart because they use syntax and semantics for better indexing, however this assumes a high degree of validity of code or else they can get hopelessly lost.
The PHPWCMS site I was going to try this on validates, but I may do some more research before taking the plunge!
I can easily delete 2 of the 3, but which one do I leave in?
According to a couple of Google forum posts, the recommendation is to leave the base URL only and remove both the '.phtml' entries.