Cannot alter theme files under development

I am having trouble with 3.1 during my theme development with a client, but when I reverted to 3.0.5, the problem went away, I’m not sure whether I should report this as a bug or if something has changed in the way things are done in 3.1.

Here’s my situation: When I do a fresh install of 3.1 and put in the theme I created, it’s all fine and good, but when I make alterations to the index.php file in my theme, those changes are NOT reflected when viewing the site or when examining the code of the viewed site. It’s as if once the theme is picked up by wordpress, it’s locked in and can’t be changed unless I keep doing fresh wordpress installs every time I alter the theme. Also, I am not running any cacheing when I make changes. Oddly, changes made to the style.css file ARE reflected on the main site.

When I reverted to using 3.0.5 for development purposes, everything seems to be working fine though. If someone could help me out to tell me if this is a bug or if there is a new way to do this, I would greatly appreciate it.

Many thanks.