It sounds like you might be confusing two different settings.
1 In the General tab, it is recommended to enable "Perform recommended actions automatically"
2 In Application Control Settings, it is recommended to enable "Load rules... Kaspersky Security Network"
Please enable both of these settings, and see if that helps.
Then, if you find any of your trusted programs that are in the "low restricted" category, just move them right back up to "Trusted," if necessary. (However, many apps will run just fine in the "low restricted" category, so you only have to do this if you run into a problem with something being blocked.)