HI Leapy.
OK I think I have got to the reason why your CBTs are being
included. If you have them at the topic level, they are exlcuded.
If you have them at the topic contents level they are included. Do
a right click on the CBT in the project tab and select the
"Properties" popup menu item. You will probably find that the tags
show up at content level. If you change these to be at topic level
you should be OK.
BTW if you are using merged webhelp there is a known problem
with links failing. Peter Grainge has covered this, and the
workaround, very well at his site. Click
here
for more details.