Is It the Windows Registry?

i had installed some software that was not particularly "safe" about a week ago. i had noticed some significant changes overall in several other programs after it had been installed. once that had occurred, i removed the culprit program from windows by performing a system restore to an earlier state. however, after the uninstallation, the problems that had been caused by the program still exist. here are a few of the problems that i have noticed and have been hoping to fix:

*Skype claims that i am not entering the correct login information even though i clearly am. before the culprit program had been installed, skype would load upon start up with no problems.
*AIM has problems with logging me in as well. it claims that there is a settings error that withholds it from signing me in.
*Nero 8 StartSmart states that "the Runtime has requested it to terminate in an unusual way"

i had initially thought that this may be some sort of error within the windows registry. unfortunately, i do not have a backup of my windows registry except for one that is several months old. i have tried to use a registry cleaner in order to find any errors in my registry. the open source program i used is called Little Registry Cleaner, which apparently found 300+ errors within my reg and fixed nearly all of them. however, it did not solve any of the problems with the software that i had previously mentioned. therefore, after this overly long explanation, i have been wondering if there is another windows component that could have been affected and that i am overseeing. is there any where else that could have affected the settings of my software? any help would be greatly appreciated!

side note: i would also like to add one peculiar aspect to the Nero 8 program. i noticed that if i search through my Program Files directory, i am able to still open each individual program within StartSmart (Nero Burning Rom, Nero Vision, etc.). just a quick fyi, StartSmart is just a program that you can use in order to access the other multiple programs that are within Nero 8. however, if i attempt to open StartSmart through the program files directory (versus the desktop shortcut), i am still given the same error message. i should also note that i did not have any success with this method for getting aim or skype to work.

To start with, download and run a scan with malwarebytes antimalware, let it clean whatever it wants.

Malwarebytes

Then run sfc scan 3-4 times.

SFC /SCANNOW Command - System File Checker

If sfc says it cant repair certain files, run a repair install.

Repair Install

It does appear the unsafe program has nuked vital reg entries, it may also have embedded malware. Dont use this computer for sensitive work right now, If after all these steps, things still look wierd, clean install windows after wiping the hard drive.