Moved this to Malware Discussions > Home User Assistance as possibly a better spot for it.
You should make sure that Java is up to date and any old versions are uninstalled. (Control Panel/Programs)
You can stop the JITD window from popping up by disabling script debugging in Internet Explorer:
-> Internet Options
-> tab: Advanced
-> in the list, under Browsing, check the box "Disable script debugging (Internet Explorer)" and "Disable Script Debugging (Other)"
-> click Apply, and OK
You may also want to uncheck the box "Display a notification of every script error".
As you've tried several malware tools you may want to download Hijackthis and post its log on one of the following forums for expert guidance:
Do not post Hijackthis logs here, we can't help with those!
Post the logs at a specialist Forum:
Be sure to read all the sticky announcements/instructions at the top of each malware forum!
The only other thing I would suggest you've already tried or so you said. A scan with a newly updated Malwarebytes, even in Safe Mode if necessary, otherwise follow the Hijackthis advice.
This is what got rid it...
TDSS is the name of the virus and this TDSS killer will get rid of it. YAY! I had to download it in the Zip file and then extract the files because the virus was blocking the regular download. Any questions, feel free to ask.
So it was a trojan, that's interesting. Glad you found "the cure".