I ran Spybot S & D Free and got 1549 files showing some sort of malware, some just adware or tracking cookies but, some show as registry files or registry keys. Should I un-check those before I click on "Fix All" or is it OK since they show up to delete thise as well. Anything "registry" makes me nervous.
Just about everything Spybot removes is backed up into quarantine.So,if Spybot made a mistake when removing anything or if anything else were to happen,it should be recoverable.Mistakes(false positives) are rare,but they happen sometimes.
Spybot also scans for usage tracks,and they also may be some of the registry keys you're seeing after a scan.Removing those shouldn't cause any harm,either,and are backed up into quarantine as well.
This is a description of usage tracks: http://www.safer-networking.org/faq/usage-tracks/
If you would prefer,you could tell Spybot not to scan for usage tracks for the time being,that should cut down on what is found after a scan,and maybe make the Spybot scan less overwhelming,until you get your bearings and get used to the program. :)
If you'd like to do that,the instructions for Spybot 2.2 are to open Spybot-S&D Start Center,click Advanced Mode,click Settings(say yes to UAC,if applicable),click the categories tab,rightclick somewhere in the categories window and select Spyware Scan only.
If you are running the Spybot 1.6.2 version and would like to try not scanning for Usage Tracks for the time being,then please see here instead:
http://forums.spybot.info/showthread.php?63976-Too-fast&p=413400&viewfull=1#post413400