Windows XP
HP Pavilion a1310y
2.93 GHz
504 MB of RAM

Yesterday I downloaded Spybot Search & Destroy because I have a trojan giving me pop-up ads and now almost all the time Myspace, Google, Blogger, and popular email websites don't load. When I selected 'Fix selected problems' it gave me the error notification box with the X: 'Failed to load D:/Program Files/Spybot S&D\Delzip179.dll' and when I pressed OK: Unexpected error in fixing problems (out of memory). The boxes kept popping up, so I Ctrl alt Delete'd and scanned again. I think after it closed I got a bunch of prompts for me to approve the change of some important registry entries, and they had to do with the path name C:/Windows/system32, but I thought it was my system infected, so I might as well accept because Spybot was repairing only problems, not making mistakes... I became skeptical so I denied the rest. The next time I reset my computer I got these windows popping up with the black screen and the grey Courier text, having to do with C:/Windows/system32... About 50 of them popped up, and some had 'Could not find ____' (complex files of sorts).

I reset my computer to clearly write down what happens. Before shutting down, I get the warning box: Access violation at address 694c5405. Read of address 694c5405' with a blank OK button. I click it...
When the computer resets the black/grey windows say C:/Windows/system32/cmd.exe, C:/Windows/system32/command.com, C:/Windows/system32/ntvdm.exe on top, and ones that says 'Could not find apkgakxk.dll_old' and some with different dll-related names. These windows pop up then disappear quickly, by the way, but take a while until I can start using programs. Then the Spybot windows pop up after THAT... They say:

Spybot Search and Destroy has detected an important registry entry has been changed
Category: System startup user entry
Change: Value deleted
Entry: Spybot DeletingB8414
Old data: command/c del C:/Windows/system32...

and some different ones.

The buttons 'Accept change' or 'Deny change'

Am I supposed to click 'Accept change'? And is this known to get rid of a pop-up trojan, or can someone tell me the solution to finally removing that?