Ok, so here was how I resolved the problem getting the error "The pages do not match! Timestamps differ or were not found!".
I was setting up a new blog, where I installed the new version of WP Super Cache (version 0.9.9.7), where I was copying the custom permalink info off of another older WordPress blog which has WP Super Cache version 0.9.9.3 installed.
In the older WordPress blog I have the custom permalink field set to "/%category%/%postname%.html".
When I copied the information into the new blog, which I have installed the newer 0.9.9.7 version of WP Super Cache, the test would not pass, giving me the error "The pages do not match! Timestamps differ or were not found!".
I played around with it for a little while, and realized that adding the customer field as "/%category%/%postname%/", (which removed the ".html", and added a "/" forward slash at the end of the text as you can see) was the solution. The 'Test Cache' ran through correctly then, and says "The timestamps on both pages match!"
Problem now solved!
I hope this helps someone else since it took me a little time to figure it out.