Blank Search Pane after certain searches

I have strange issues after migrating from Robohelp 8 to Robohelp 9. Neither of these issues come up if I view the project in Robohelp HTML before publishing, only after I publish with WebHelp Pro do these come up.
I have some searches that say they have found no results when in Robohelp 8 it returned over 20, most of which blatenly have the search word in the title. I have confirmed these articles exist in both, just cannot search them in robohelp 9
Exact same project upgraded and published from 8 to 9
First image: Robohelp 8 and Robohelp server 8
Second Image: Robohelp 9 and Robohelp server 9
I have very specific search strings that when you search for them the search pane goes blank and will not return until the page is completely refreshed.
I have viewed the source, there is a bunch of JavaScript stuff but not <body> tag to be seen.
I have confirmed there are no illegal characters in the filenames in my project.
Anyone have any idea how to resolve these?
Thanks for any help you may have, even wild guesses could help at this point.

New info, hopefully this info will spark an idea for someone
robohelp_server.properties
substringsearch=true
will resolve issue 1
issue 2 remains
reindex=true
will resolve both issues
this however makes context show (see http://forums.adobe.com/message/4807874#4807874)
I discovered that issue 2 is caused by the word "not" being in the search, substring search and the work "not" dont seem to get a long.
So I can get it working by going reindex=true, I would however prefer not to if we can resolve the issue 2 "not" issue

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Blank Search Pane after certain searches

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