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Welcome to the forum.
There is nothing I know of in RH that would have that effect on your source files. When you generate webhelp there is an option to generate your help with lowercase file names. Is that box selected in the first page of the wizard?
I believe it is generally regarded as unnecessary to check output files in and out but will leave someone else to confirm that.
Oh, yes - I can confirm that it is generally not considered necessary to put output files under source control, except in one circumstance. (Which I was unfortunately caught up in.)
If your application does automated builds from the source control system, the build script can't generate WebHelp - you have to open RoboHelp and generate from there. In that case, I had to generate my WebHelp output and check the whole thing in.
I got around the filename thing (because adding/deleting topics was causing merry hell) by packing the whole output folder in a .jar file - kind of the Java equivalent of a .zip file. The build script could unpack the .jar and put the help folder where it was supposed to go.
This happy solution took about three months to come up with - the first one was for me to beg the forum for a command-line compile for WebHelp (duh, it's proprietary, so there isn't one), the second month was to convince the ClearCase dudes that there wasn't a command-line compile for WebHelp, and the third was persuading the ClearCase Powers That Be to let us check in the output .jar. Oy!
Hello Tara -
Doesn't sound like an RH issue but a source control issue. This from Answers.com:
"In order to compare data properly, in applications of all kinds on all platforms, it is common to convert user input and data from the database to the same case before the comparison is performed. It does not matter to which case the letters are converted as long as they are the same case. "
...or is it the other way around for you. That is, the files COME from your source control with your desired case mix but once in RH it converts to all lower case?