I ended up having a similar issue as originally described by heffevuna & planitDocs. I did attempt the solutions described by planitDocs and the only one that seemed to make a difference was to remove the XML declaration from the beginning of each topic. Sadly, this has to be done manually outside of Flare (post-processing).
I've put in a help request and it seems that this is indeed the issue. There apparently is some system setting which results in the HTML Help View not properly displaying anything beginning with an XML declaration. This may be some third-party software which associates itself with opening XML files or some security setting; MadCap tech support hasn't yet identified what exactly. It does appear that resetting IE to the defaults corrects the issue, but it may not always be easy to convince a user to do so (particularly, as previously stated by others, if they have higher than default security settings in place).
However, as removing the XML declaration does no harm to the HTML files in the compiled HTML help, I have requested that an option--similar to that available to remove the DOCTYPE declaration--be added for HTML Help targets. I've been told this has been passed on as a feature request. As this is (seemingly) something easy to implement, it could be added in a future update; particularly given the extra manual effort to clean these up is tedious.
But, for the sake of thoroughness, my process is this:
1) Build the HTML Help target in Flare normally
I don't know that the DOCTYPE declaration option has any affect on this issue, but it doesn't hurt to just leave it out as well.
2) Locate the temporary HTML Help project files:
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{Flare project location}/Output/{user name}/Temporary/(Flare project name}/Content/
3) Use RegexBuddy (or some similar bulk file search & replace tool) to comment out the XML declaration from each HTML file in the project
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<?xml version="1.0" encoding="Windows-1252"?>
(If you neglected to remove the DOCTYPE declaration, it can be removed in the same process)
4) Open _Temp.hpp in Microsoft HTML Help workshop and recompile. Redistribute the new CHM output from the same temp project folder.
-Jason Coleman, P.E.
Sr. Manager Technical Content
Bentley Systems, Inc.