Matthew and Dirk are certainly pointing in the right
direction. Microsoft never got around to squashing all the bugs in
MS HTML Help. If you are working with secondary windows I highly
recommend prefixing all window type names with "$GLOBAL_". I always
do that as standard practice as it was recommended by Microsoft's
lead developer of the .chm format, Ralph Walden. You can easily do
this in RoboHelp's Window Properties dialog. So if your window name
is "Secondary_Window" you would rename it
"$GLOBAL_Secondary_Window". I put the prefix on all window names
for good measure.
For more info, try Rob Chandler's site
http://www.helpware.net/htmlhelp/how_to_merge.htm
Click on the link "Secondary Windows" for the good parts.
One final thing, you probably already have, but be sure to
download the latest service release so that your version should
read X5.0.2. Updates are here:
http://www.adobe.com/support/robohelp/downloads.html
Hope this helps.
john
John Daigle
Adobe Certified RoboHelp and Captivate Instructor
Newport, Oregon