In the past we have seen this issue when users encountered issues during the patching process. In particular they did not have write access to the ~\config\security.xml file and as a result the new entry for the LDAPAuthenticationProvider is not added. If you open your security.xml file do you seen an entry similar to the following? If not please try adding it manually.
<provider default="false" type="authentication" name="LDAPAuthenticationProvider" filePath="FULLY QUALIFIED PATH TO CHECKBOX INSTALL DIRECTORY/config/LDAPAuthenticationProvider.xml" configDataType="Checkbox.ActiveDirectory.Providers .LDAPAuthenticationProviderData,Checkbox" />