Your problem is probably the definition of the subdomain in your HTTP Server where you have provided the master path instead of the same "deployed directory" where you have put all the links.

If you are using a cPanel,
suppose that www.domain.com is located at /home/account/public_html
and that the slave site is slave.domain.com that is located at /home/account/public_html/slave

then when you define in JMS the "slave.domain.com" you have to deploy it into the "/home/account/public_html/slave"

I suppose that you have not correctly defined the HTTP Server and that perhaps you have just modify the DNS to provide a synonym (cname) between www.domain.com and slave.domain.com

I just bought this component for a client. I slaved the a site out and I'm having the same problem. The deployment directory is correct but the Custom Modules and Articles cannot be edited. Did you find a final solution?

Please describe your problem in detail.
We don't have any issue pending.