A couple weeks ago, I started getting pop-up ads on websites I frequently visit. I typically Chrome or Opera and only use IE when necessary. I also run AdBlocker Plus. Avast hasn’t alerted to any attacks, and an Anti-Malwarebytes scan didn’t turn up anything. Now I’m wondering if I picked up something malicious that’s not turning up on a scan.
You may install add-on for each browser that you use which is from each browser has providing the add-on tools to protect that.
Have you try to run boot-time scan with avast!?
For each visited website, you may scan with :
Schedule a boot time scanning with avast with archive scanning turned on. If avast does not detect it, you can try DrWeb CureIT! instead.
Use MBAM (or SUPERantispyware or even Spyware Terminator) to scan for spywares and trojans. If any infection is detected, better and safer is send the file to Quarantine than to simple delete them.