I encountered the same problem a few times. Installed default dictionary and .opf file settings were getting over-ruled in the spell check. The cause turned out to be meta tag settings in each html page, like so:
Code:
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops" lang="en-us" xml:lang="en-us">
Check to see if that is what is going on here.