I have a program launching a website via the following command.
cmd \"start /max http://url.com\"
When launching a website via this method
IE has a setting, located in Tools / Internet options / Advanced / Browsing, called Reuse windows for launching shortcuts, which is checked by default. For IE versions that support tabbed browsing, this option is relevant only when tab browsing is turned off (in fact, IE9 Beta explicitly mentions this). However, since IE6 does not have tabbed browsing, this option does affect opening URLs through the shell (as in your example).