SkySync will always use IE whenever a web based connector is being created that requires login. Additionally SkySync does not have it's own imbedded browser and instead uses the version specified by the computers registry. Sometimes when a custom SSO is being used script errors and other issues can occur during the connector creation. If that is the case it is possible that the web browser version specified in the registry is too old.
This link provides instructions on making an adjustment to the registry. It should be kept in mind that making changes to the registry have inherent risks and that by making these changes you understand that SkySync is in no way liable should an damage to the computer occur.