Missing Programs from Programs and Features List after Virus.......

I recently got a virus on my computer which luckily I was able to catch. Microsoft Security Essentials did its job and caught the virus, and ALL my programs work just fine to my knowledge. The only problem I am now having is that some of the programs I have installed on my computer and work fine does not show up on my programs and features list, I have done everything I know how to do. At first I thought it could be a Registry Error, so I found a reliable tool to can my registry.....no problems. I thought it might be spyware or malware, which I use the paid version of malwarebytes-Anti Malware, no problems there either. I also downloaded the tool from Microsoft to scan for malware and any other bugs but came up empty. Does anyone know what is causing this and how to fix it?

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