I'd suggest setting up an alias with the .aspx extension then for those pages in question. Also ensure you have your settings correct in Site Manager. Specifically the Redirect document aliases to main URL property.
When you navigate to those pages, where are the URLs created? Are they in an editable text webpart or somewhere else where it is not dynamically generated?
The pages in question, do they have forms on them or something where you'd post back? If you'd need to add this web.config key
<add key="CMSUseExtensionOnPostback" value="false"/>