I'm using SF version 3.7.
I've tried recompiling the site to no effect also restarting IIS, again no effect.
I have master pages in the app_master folder which are being used as templates within sitefinity. Everything works fine when I upload a new master page and set a page to use it....pages display correctly, content place holders are fine etc.
If I then make a change to some html in the master page in VS2008 and save the file this has no effect on the template within SF. Of course if I use this master page in a regular aspx page within VS everything is fine, and the changes take effect.
The only way I can get the changes to take effect is to upload a new master page and then set all my pages to use that template, which for a large site is obviously not an option in the long term.