I've been having this problem with previous versions before 2.9 of WordPress.
If I have "1st visit mobile users will see desktop theme" checked then when users visit the site with an iPhone they get the mobile version, which is fine, but they can't switch to the 'regular' version of the site. Clicking the 'Mobile Theme' slider on the bottom just brings them back to the WPTouch site.
If I have "1st visit mobile users will see desktop theme" un-checked then users get the normal site. If they click on 'Mobile Theme' slider on the bottom it brings them back to the normal site, it won't go into WPTouch version.
I've also seen problems where if a person is in the WPTouch version of a post, hitting the top title to go back to the homepage takes them to the 'regular' website out of the WPTouch theme.
Disabling HyperCache appears to solve the issue. Are some settings for HyperCache that are knows to make the combo work?