Can I move distribution profile modules from profile folder to sites/all/modules? I just installed a distribution profile and ran Drush up to update modules.

I have some problems with the modules located at profiles/somefolder/modules: Drush moved out the old modules but no new modules are added.

Can I move the modules from profile folder to sites/all/modules? 

The installation profile is Commerce Kickstart.
If the modules in question are not enabled you can move the modules.

The paths to their location in the system table in the database will be updated when you visit /admin/modules.

However, If they are enabled you may run into issues. 

See http://drupal.org/node/183681