This sounds like the same caching problem that others have reported here with their internet provider. I would check with whoever is hosting your application and see if they are caching the files and not updating them right away. I have never seen this behavior with ClickOnce.
If you can run IIS on your machine, try deploying it locally, change something, deploy it, repeatedly. Install it locally the first time, then run the app to pick up the updates and see if it works. I'd bet this will be successful.
To deploy it locally, set the publishing file location to http://localhost/yourappname. You can use that url to install it on the same machine. I actually test the installation on another machine on my network by specifying the installation url as well, and fill in the IP address instead of 'localhost', like this: http://123.456.788.999 /yourappname, where 123.456.788.999 is the ip address of the machine I'm running IIS on.
Give this a try, and it will clarify where the problem is.
RobinS.
GoldMail.com