Welcome to the forum.
Webhelp is three frames, the toolbar, the TOC and the topic.
I take it you are seeing two frames for the topic. If that
does not happen when you open the startpage, then it is something
that the configuration team are doing wrong. The fact that you
generated to a folder other than the default should not affect
anything, provided you generate (as opposed to publish) to a local
folder.
Spaces have caused some issues in RH7 but that was fixed in a
patch. I doubt it would cause this problem.
Have the configuration team all the files and folders
generated. Sometimes they think only some are needed.
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