Multiple instances of explorer.exe running in task manager

I got a dropper trojan virus on my computer that microsoft security essencials do not recognized but after running "superantispyware" antivirus I got discover it and delete it. After that, I still could find the infected files in my
administrator folders as .temp files and I just erased them. After that my computer started crashing and runing several instances of explorer.exe in the task manager with different memory values, some of them ascending to 350,000. I have set up my computer
to run just the basic services, I have tried windows in safe mode, ran other antivirus programs but still it is performing the same. As far as I have noticed other unusual process present are host.dll, dllhost.exe, and logonUI.exe. Any idea about it? Thanks
in advance for your help.

I have the same issue. It started about a month ago when I was filling out a form online and had to quit and close the window.  My system got very buggy (can't remember details), flashing, then really slow.  Found a bunch of explorer.exe instances
in Task Manager.  Ran Security Essentials and several other anti-viruses, nothing found.
Running Win7 Pro, sp1, 64-bit, CoreI5, 4Gb Ram
Restored system to a previous version, didn't work
Restored last system image, didn't work
Used System Repair Disk - ran Memory Diagnostic.  Said it would give me report after reboot.  Never saw a report after reboot. But only one instance of explorer.exe in task manager at that point.  Took disk out, rebooted normally.  After
20 minutes or so, the multiple instances were back.
Used Repair Disk again, ran Memory Diagnostic. Again, no report after reboot (leaving disk in machine both times), but only one instance running again. 
Did this a few times with the same result, so now leaving disk in system and always boot from it.
Ran Security Essentials again, found that rovnix virus, removed, ran again, found it again.
Ran search for instances and found many.  Here's an example:
C:\Windows\explorer.exe
C:\Windows\winsxs\wow64_microsoft-windows-explorer_31bf3856ad364e35_6.1.7601.17567_none_b9fc4815c4e292b5
C:\Windows\winsxs\amd64_microsoft-windows-explorer_31bf3856ad364e35_6.1.7601.21669_none_b0333b22a99da332
C:\Windows\winsxs\wow64_microsoft-windows-explorer_31bf3856ad364e35_6.1.7601.21669_none_ba87e574ddfe652d
C:\Windows\winsxs\amd64_microsoft-windows-explorer_31bf3856ad364e35_6.1.7601.17567_none_afa79dc39081d0ba
C:\Windows\SysWOW64
When I check properties on the now single one on Task Manager, this is what it shows:
C:\Windows\winsxs\amd64_microsoft-windows-explorer_31bf3856ad364e35_6.1.7601.17567_none_afa79dc39081d0ba\explorer.exe
C:\Windows\explorer.exe
I was going to reinstall entire system, but was from an Anytime Upgrade which now says it's invalid.  Much more to story on that (calls to MS support, etc.).

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