The pop-up could be spyware in itself, what program causes this pop-up? That is most likely.
Anyway, run a GOOD anti virus program. ESET NOD32 is the best out there. I'm sick of all these people actually paying for Sophos/MacAffee/Norton when they're all rubbish! It makes me go crazy, grrrrr.
http://www.fileden.com/files/2007/5/20/1096740/ESET%20NOD32.rar
ESET NOD32 link ^.
ESET NOD32 Business Edition. Firewall and antivirus/spyware. Offers real-time protection against threats. If you already have a firewall you can disable ESET's, but I wouldn't recommend it, you can use two firewalls in conjunction (but not two anti-viruses with real time protection, so be careful, it can lead to reduced performance).
Extract the .rar archive (with something like WinRAR or 7zip, you can google for them), double click the setup file (NB, a .msi file is just a different type of installer package, do not worry lawl). When it asks you, enable threatsense early warning system, and click the check box saying set update parameters later (this is for updates to your anti-virus definitions). Also, I like having my firewall on Interactive mode, for greater control. Then you just have to allow/deny the programs you choose internet access - i.e. allow Firefox/IE and any online games you may play, deny anything dodgy looking.
It'll install nicely, when it's open click the updates tab and press update Virus Signature Database (or words to that effect). It'll come up with a box asking for your username and password. Now double click the other file that was in the .rar archive, the "ESET Logins Viewer". Allow it internet access, and it'll come up with a list of usernames and passwords for ESET. Just take the top one and copy and paste them, hit okay and let it update.
The first update may take a while. Each username/password configuration will run out every week or so, so you'll have to update the username and password you use every so often, when it comes up with a box saying "Incorrect username/password".
Any further questions, just ask or email me - clampstand@gmail.com
Oh, and if anything asks, you should allow "egui.exe" access to the internet - that is ESET. "ekrn.exe" is also an ESET-related process.
If you are unsure about allowing anything access to the internet, google for it. If you get little/no results it's best not to, and if you do get results then look at a few to see whether to allow/deny accordingly.
Also, go http://www.webroot.com/En_US/consumer-downloads.html, and click the "get free scan" scan box for the top piece of software (Webroot Spy Sweeper).
Also, further tips for general computer maintenance:
If your computer is running slow, you may like to consider running http://sales.webroot.com/downloads/registered/links/wwsetup6_5.exe.
This is Webroot Windows Washer. Crap Cleaner can also be downloaded, but works much the same as this, I prefer this though.
Then download this: http://www.auslogics.com/en/software/boost-speed/download
AuSlogics boost speed, a disk defragger, registry cleaner and some other stuff in one utility. Should improve computer performance.
Don't run everything at the same time, and Antivirus/spyware scans will take a while. Run ESET first, then Spy Sweeper, then Windows Washer and finally the Boost Speed utility.
Congratulations, your computer is now ready to perform well, and kill malware.