So I am a little worried eset found so many corrupt files after performing the aforementioned tasks. Should I run a random virus/malware detection program from time to time?
Absolutely!
You should update and run MBAM every couple of weeks - more often if you engage in unsafe internet practices.
Keep a good AV/Firewall combo updated and running at all times. There are many good and free options available.
Online scans such as ESET are a good "backup" to your resident AV program if you feel you need a "second opinion."
The stuff ESET found is not worriesome.
You are going to get adware (or worse) in a lot of codec packs. I would recommend downloading them from a site such as Majorgeeks.com. The site owners are very good about keeping their downloads free of malware and crapware.
The Kryptik trojan was removed by combofix. What ESET detected was the combofix quarantine - no worries there.
To avoid these types of malware, always keep your Java updated and always remove older versions. If you automatically update it, this should be done for you.
Also, running ATF-Cleaner will flush the Java cache (if you set it to do so as directed in the Read Me First post).
The other detections are in System Restore. The combofix uninstall routine should have flushed System Restore points, or, at least it used to.
You can do this manually by turning System Restore …