You should verify that you have built the merged package
correctly, which results in a set of folders (Leon names them
above) in the master project folder that contain data for only the
master project, and a set of data folders of the same names in each
subproject folder.
Your master project must have its own index, even if there's
only one term.
WebHelp, in effect, combines the master index and sub-indexes
when the launch page loads.
I haven't tried merging projects when one or more, but not
all, had an index. I'm guessing you are missing a master index
(unless Leon's hunch was correct, and someone moved or eliminated
"redundant" files).
Please post back on your results.
By the way, are you saying Windows vs Unix seems to be the
primary factor?
Harvey