So I figured this one out, JoomSEF is really nice if you know how it works, ok now this is what I did:

1. in JoomSEF under "Configuration"
2. in the "basic" tab, enable professional mode, then
3. under "advanced" tab, (bottem right)
4. -> Exclude source info (Itemid) = Yes
5. -> Reappend source (Itemid) = No
6. -> Ignore multiple sources (Itemids) = Yes
then
7. -> go to "Manage SEF URL's"
8. now on the pages where you have missing modules, click on the SEF URL to enter the properties
9. under the "URL" tab there is a text box which is "Itemid" over there you need to enter the ID of the Menu Item, you can fond that under "Menu Manager: Menu Items"

Following this steps fixed the problems.

Hello, I have figured out that some of my modules are not showing due to JoomSEF managing the URLs, on the FAQ page number 12, www.artio.net/de/product-faq/joomsef-faqs#faq12 they mention

"The problem is most likely caused by incorrect Itemid set for SEO URL." and that I can

"control the way JoomSEF handles this variable using "Exclude source info", "Reappend source info" and "Ignore multiple sources" options in configuration or with some options in extensions' parameters."

I have enabled and disabled the options in the configuration and one of my menu items doesn't seem to take effect with displaying the module, the FAQ page there must be a blue banner kind of thing like the other pages.

I wonder if I can ask someone how I can configure this program so that the modules are displaying correctly?

Noted,
Regards,
Lloyd

Hi, I just wonder, when I look in my "JoomSEF URL Manager" > "Manage SEF URL's" I see allot of links and as I am still developing my site, I have allot of dummy articles and they all receive url's, and some of those articles get deleted, and then I have allot of url's, which (as I undestand) is like "dead" information, how can I filter that out and delete them? I like to have a clean website...