Have you packaged Internet Explorer and gotten the default browser popup when testing your ThinApp package on another Windows system?
No worries, here is how to disable that popup for your ThinApp package.
Disable During Capture:
You can disable it prior to harvesting Internet Explorer 6 from an XP Pro system (or during capture of Internet Explorer 7/Internet Explorer 8) by launching the Internet Control Panel Applet by typing INETCPL.CPL in the RUN line after Pre-Install Setup Capture but prior to the Post-Install Setup Capture (when you would normally install any other app to capture). You'll then want to browse to the PROGRAMS tab and uncheck the "Internet Explorer should check to see whether it is the default browser" check box.
Disable Within Project:
You can also disable it within your Internet Explorer ThinApp project after the fact as well as this is simply a registry modification to the project. To do this, edit the HKEY_CURRENT_USER.TXT file and add the following data under the HKEY_CURRENT_USER\SOFTWARE\MICROSOFT\INTERNET EXPLORER\MAIN key.
isolation_full HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main
NOTE: Do NOT add the registry key (as most likely it is there already). Rather, just add the VALUE and REG_SZ lines (shown above) underneath the registry key line. You'll probably want to search on "HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Main" and see if there is a "Check_Associations" value already defined with a value of "yes" instead of "no". If it's not listed, add it to the bottom of that section...and make certain to leave a blank space between the bottom of that section and the top of the next section.
Once done, save and rebuild!