I never figured out what the cause of the issue was but to fix the debug
problem (the creation of the second window) I created a new work space,
reset all my preferences, and copied the projects from the other workspace
into it. Once I did this I was able to modify my code, add and remove
break points while debugging. If anyone ever figures out the issue please
post it here.
Thansk,
Ben
PS: I tried to post this under web tools per the previous response but
could not find the link to that newsgroup anymore.