Sorry for the delayed response. For more timely responses, please post any problems in the support forum (as indicated in the plugin) where I will be instantly notified rather than need to check here.
@vesket, Just to be sure we're on the same page here, you are referring to the plugin by Alex Rabe, version 1.3.3 correct?
The Clean Options plugin does not have a "fix automatically", what exactly are you referring to?
It may be that there is an incompatability issue. I will look into it.
However, note that this plugin does not list only orphaned options, but rather options that appear to be orphaned. That is, the plugin will find true orphaned options, but may also find options that, as looked for by the regex used in the plugin, will appear to be orphaned when in fact they are not.
The Clean Options plugin is written so that as best as is possible, WordPress Core options can not be accidently deleted. However, it is impossible to take into account all possible options from all possible plugins and themes. Thus the need for blogmasters, that hopefully have knowledge of their blog's particular plugin history, to investigate options in the list of possible orphans before removing them.
The plugin has several ways to help users in identifying true vs. false orphans. All measures should be taken before any option is removed. Only when when it is certain that an option is truly an orphan should it then be removed.