My attempts to open the new/converted LyX file cause a message (this is a translation; it may be not exact):
"The class cannot be loaded. As a result of the error in the document class file: ijnam could not be loaded. A default document class will be used with a default layout. LyX cannot produce a correct result". The file is then opened, but indeed the file structure seems to be different from the intended one. I stress that in my opinion the class has been installed correctly, as it works with TeXWorks. Also, there were no messages of this sort previously, before installing your layout file. So, I would rather suspect that something has to be changed in the layout file. My inability to import the original TeX file into LyX (after installing the layout file) seems to confirm this idea. Leslaw
