Boot Time Virus Scans? What software?

Completely unnecessary. Why would you even need this?

For peace of mind, you can try Avira. Avira does a CD-based Anti-Virus program. It runs off the CD and does a scan without booting into Windows. The file is updated regularly.
 
Boot time scan because when I used to run XP I found Avast to be usefull, as it found items during a boot time scan which did not show up on the live scan with Windows running.

Sadly Avast does not do a boot time scan with 64bit software.

May be unnecessary, I thought that yesterday when I was attempting to get rid of what looked like a trojan runing under a Java pseudo, with what may have turned out to also be related to Avira and MSE fake pop ups.

Running Comodo, Avira, Avast, Malawarebytes, SuperAntiSpyware, Ad-Aware, Microsoft Security Essentials and CCleaner yesterday (including within safe mode) did not get rid of it as the issue again reared it's head today, again I ran all the above and it seems to have burried it's head under the sand but I have no way of knowing if it will pop up again?
 
No, there was an Avira pop up which had a lower resolution icon, it popped up next to the Avira Icon on the task bar and it was clearly more blocky which has me thinking fake.

I posted a picture up of the MSE pop up, it only came up after Comodo found a single file, but the MSE pop up showed the same Java related files as the posibly Fake Avira pop up. These Java files seem to be known as Trojans as they are on Google as such?

During all this a few pop ups happened which may have been genuine and my Avira went offline and showed no option to re-start so I uninstalled and re-installed this but it again showed up off with no on option, I also uninstalled Java and it appeared in my task bar while uninstalled but as of this afternoon I seem to have been free of problems and slow ups etc.

I had to re-install Java to open my Photobucket to upload the JPG I took.

Sadly running Avira boot disc does not work on this machine (on which I downloaded the Iso and created the disc), when it does come on screen I don't get the little animal with a strap on yellow beak either?

I ran all these anti virus seperate and together, in fact they seem to be running fine together at the moment, Ad-Aware, Avira, Microsoft Security Essentials, Avast and Comodo are all running at this moment in my task bar, just slows boot time a little.

Some of the issues seemed to say there was a virus, computer re-booted when I was trying to resolve issues, Avira had updated yesterday but when ran it showed as needing updated and offline. It got so bad I did a system restore which ended up with me having a black screen and mouse pointer then doing a later system restore and redoing everything just to have it rear up again today and me go through the methodic everything all over again.

Maybe I am just being paranoid, though tempted to just save my files and start again with a fresh install.

Still have no idea what happened and how nor if it is gone or not, will I have to secure erase the HDD to ease my mind :(
 
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