Permalinks all messed up, I am helpless [closed]

Today I tried to make the Permalinks of my WordPress site more SEO friendly. I got it working for all links, except the ones linking to a custom post type page. I Googled the problem and found out that it’s a common, in my eyes not-so-easy-to-solve-type problem. That’s why I wanted to use the default permalink structure again (I am still in development phase).

Now nearly all links are broken! Sometimes I get a 404, sometimes the browser itself says “page not found” – on some links, the default structure is still working. When I manually try to get to a page by entering the id manually in the brower’s address bar, the address changes to the new structure, but I get a 404.
You see, something is all wrong there and I don’t really know how to fix it. I read about editing the .htaccess or httpd.conf (I’m in XAMPP) file, but because I don’t know anything about this, I don’t really want to change anything in there.

Is there any way of “resetting” all permalinks to their default format?

Edit:

Ok, according to the comments I should post the rewrite rules.
Problem: I don’t even know what exactly to post from there!

Plus one funny thing happened: I set the Permalink structure to /%postname again (since I am in 3.3.1 this should be alright I guess) and now it is working again. Only one link (the link to the custom-post type) is still ugly. So now I am in the same state as a few hours ago – although I still don’t understand what is going on.

When everything is correct, a URL looks like this:

http://www.example.com/kitchen

But for a custom post type, the URL looks like this:

http://www.example.com/?food=food

or when I visited

http://www.example.com/kitchen

before that:

http://www.example.com/kitchen?food=food

I use a the custom-post-type-ui plugin to create the post types.

Please tell me what I should copy (I mean, that’s a pretty long list right now…), then I will post it, but I just don’t know right know. I guess that’s why I can’t even precisely describe the problem above, I am sorry!

Edit:

The .htaccess looks like this:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /wordpress/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /wordpress/index.php [L]
</IfModule>
# END WordPress

There are probably more problems with your question than with WordPress. To get an insightful answer, it’d help to get us a clear idea about your setup. Don’t be shy about hiding your website link and it’s structure. This can help us figure it out.

To get the rewrite rules of your blog

add_action ('template_redirect', function() {
  global $wp_rewrite;
  var_dump($wp_rewrite);
});

That should help as a starting point.