Why are my mods not working after I install them?
When installing mods from the "Steam Workshop" it is going to attempt to write the modID entry into your "Sandbox_config.sbc" file of the save you have specified in the "World Name" section of your "SpaceEngineers-Dedicated.cfg" via "Config Editor".
If the "World Name" section in "Config Editor" does not match what is after "\Saves\" of the path section in your "LastSession.sbl" the installer will not be able to write to the correct file as it does not exist or is not the correct save being loaded.
To correct this open your "LastSession.sbl" in "Configuration Files" with "Text Editor" and look at the path section: <Path>C:\TCAFiles\Users\username\123456\ServerSaveData\Saves\MyWorld</Path>
The specific spot you want to look at is just after "\Saves\", in the example above the save is called "MyWorld".
Once you have specified what save is being loaded by the server go back into your "SpaceEngineers-Dedicated.cfg" config file via "Config Editor" and change the "World Name" section to that save name that is being loaded OR update the aforementioned "LastSession.sbl" file to load the world name that is set in "SpaceEngineers-Dedicated.cfg". If you update "LastSession.sbl" to a new world name, please note you will have to start the server at least once in order to generate the world's saved file (where the mods are written to).
Once you have made the change save your config file click on the "Steam Workshop (installed)" icon then click "Reinstall All" at the top.
Wait until the process has finished then start your server.
While your server is starting you should be able to see mods downloading in the "Web Console" which means your mods are officially installed.