This is caused by you creating .iso files using the ISO-9660 standard.  If you do this, then all filenames will be converted to uppercase as this is what the standard defines and also, filenames will be 8 characters long with a 3 character extension.  Longer filenames will either be truncated, or end up with a tilde in them.  (DOS 8.3 format, I think)

Anyway, if you want to create an .iso so that it contains filenames longer than 8 characters, then you need to create a Joliet CD.  Since I am new here, but know a great deal about CD formats, I know this is what is causing you problems.  What I do NOT know is whether WinCDEmu supports creating such CD’s.  It should though.  Also, you should specify what you want to use the ASCII character set too, as the ISO standard only supports uppercase characters.

Personally, I probably wouldn’t use WinCDEmu to create .iso images and use something a bit more dedicated to the task.  Software such as Nero, UltraISO or PowerISO are the things you need for really creating compliant .iso images.