problem with permalink (redirect to main domain)

I recently installed WP on my GoDaddy hosting (in my root directory) corresponding to MainDomain.com. As I wanted to have other blogs for different domains, I installed the Multisite version with the subdomain option (as my blogs have nothing to do with one another and I didn’t want the nested -i.e. subfolder- option).

As for now, I have two different domains in my hosting:
1) MainDomain.com
2) OtherDomain.com

They’re both pointing to the root directory (it was the only way to get them both to work with WP), as opposed to what is advised for multiple domains in one hosting.

I don’t use any posts, just pages. I don’t have any plugin running.

Problem:

– When using permalinks in OtherDomain.com (i.e. OtherDomain.com/page-with-pretty-permalink/) I get redirected to MainDomain.com
– Non-existing pages in OtherDomain.com get redirected to MainDomain.com, instead of the 404 template I set up for OtherDomain.com
– Permalinks in MainDomain.com work fine, and non-existing pages in MainDomain.com go to the corresponding 404 template
– Permalinks of a nested blog, MainDomain.com/OtherBlog/, work fine and non-existing pages point to the 404 template of that blog

So, the OtherDomain.com site is the only one not working fine for permalinks and non-existing pages. It does work if I navigate through existing pages with the ugly links (OtherDomain.com/?page_id=xyz).

My .htaccess file’s content is:

# BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ – [L]
RewriteRule ^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^[_0-9a-zA-Z-]+/(.*\.php)$ $1 [L]
RewriteRule . index.php [L]

# END WordPress

I would also love to be able to point OtherDomain.com to a different folder in the server (instead of having two domains pointing to the root folder), but right now if I do that I’ll get the GoDaddy 404 template (even if I put a copy of the .htaccess file in that folder).

I’m obviously no expert here but I’ve been searching the whole internet for a solution since two days ago, have changed the .htaccess file several times and have tested several other things, but NOTHING works. This is just sooo frustrating…

Please help ??