MS registry mutilation using a registry cleaner:

Registry Cleaners have their own disadvantages like poor distinction feature. However, some Cleaners easily make distinction about the severity of errors but they fail to rate errors and usually classify them critical without any reasonable ground for claim.

What are the drawbacks of Installing Registry Cleaners:

Critics often claim that there is no authentic way of knowing whether a third party application has an invalid key, redundant information or not.

Inefficient and poorly crafted Registry Cleaners could not make distinction between used and unused key for Windows. It could not assess the detrimental effects of removing used key from computer.

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The abovementioned flaw in Registry Cleaners create some worrisome situation such as malfunctioning of system, loss of functionality and accessing Microsofts application compatibility updates to prevent harmful Registry Cleaners.

Registry Cleaners have their own limitations for instance they cannot correct scenarios like undeletable registry keys owing to insertion of null characters in their names. Some specialized tools such as Sysinternals (now Microsoft) and RegDelNull utility can perform this task.

Potential to Recover:

A registry hive, which a system is unable to mount, cant be repaired by a registry cleaner.

However, there are several ways supported by Microsoft to repair a corrupt Registry. For example Automated System Recovery feature of Windows XP wherein last Known Good boot menu is achieved by using System Restore or by running setup.

Removal of Malware:

Despite all these problems, a corrupt registry can be recovered in several ways supported by Microsoft. For instance Automated System Recovery by using System Restore or by running setup from the Last Known Good boot menu.

Registry Cleaners fail to detect or delete Registry entries linked with a rootkit that can conceal this information from other processes.

To draw a comparison between the results of Registry API and raw underlying Registry storage, a specialized tool is required.

Do Registry Cleaners work in application virtualization scenario?

Registry Cleaners prove inefficient in case of virtualized application because all the Registry entries are written for virtual Registry. This virtual Registry is specifically designed for a virtual application instead of real one.