The new Drupal 7.5 update has caused a lot of issues for everyone regarding modules the system feels were not uninstalled correctly.  I am using Official, and I did uninstall some custom modules the client did not need.  They were uninstalled correctly however this update has issues with that.  For the most part, simply re-uploading the modules to the correct place, then uninstalling in Drupal, then removing the directories has worked fine, except for Official theme.

Drupal will not recognize the custom modules, uploaded into Sites/Modules, or Custom, or even Contrib folders.... it wont see them no matter if I put them in the correct loaction or in the main directory.  So I cant clear these errors.  

I am hoping you have some suggestions on how to reinstall the modules so I can uninstall them again and clear these errors.  This is happening with CUSTOM MD_modules only... all the normal contributed modules have behaved as expected.

See Errors Below:

• User warning: The following module is missing from the file system:md_official_about_us. In order to fix this, put the module back in its original location. For more information, see the documentation page. in_drupal_trigger_error_with_delayed_logging() (line 1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_commerce. In order to fix this, put the module back in its original location. For more information, see the documentation page. in_drupal_trigger_error_with_delayed_logging() (line 1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_commerces_features. In order to fix this, put the module back in its original location. For more information, see the documentation page. in _drupal_trigger_error_with_delayed_logging() (line 1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_commerce_features_module. In order to fix this, put the module back in its original location. For more information, see the documentation page. in _drupal_trigger_error_with_delayed_logging() (line1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_demo_features. In order to fix this, put the module back in its original location. For more information, see the documentation page. in_drupal_trigger_error_with_delayed_logging() (line 1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_skill_features. In order to fix this, put the module back in its original location. For more information, see the documentation page. in_drupal_trigger_error_with_delayed_logging() (line 1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_testimonials_features_module. In order to fix this, put the module back in its original location. For more information, see the documentation page. in _drupal_trigger_error_with_delayed_logging() (line1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc).

• User warning: The following module is missing from the file system:md_official_testimonial_features. In order to fix this, put the module back in its original location. For more information, see the documentation page. in _drupal_trigger_error_with_delayed_logging() (line 1153 of/srv/bindings/b5aadf6e5d024e41bd5d70e30116f3d1/code/includes/bootstrap.inc)