I just took my computer in to have malware removed. They did a good job with that and now things are running better. However, now my Midi interface is not listed. When I open Sonar X3, I'm told the Midi devices cannot be found, and does not list them . In Preferences, the Midi interface is not listed at all for input or output. (Actually, at one point, I saw one of the two ports but it only worked for input - I since rebooted and do not see anything again).
 
Windows Control Panel of course tells me the device is working properly. Drivers are up to date. This has worked fine for a long time, even while the malware was still on the system. I just got it back cleaned up and they are gone. What can I try?
 
Specs in signature.

Ah, ya, did it mess up the registry with the malware?
Did you right click on "Computer" and get up Properties and get up the tab "Tools" to check your harddisk?
If on the "C:/" Primary partition, you will have to do it (Windows check the disk) when you start the computer?
Any other partition can be done while in Windows.
Did they delete any System Restores on the computer to make the malware is not lurking on anything for sure?
Might be wise to just do that anyway and after all done, then do a new System Restore.
Any drivers for the MIDI?
If so they may be corrupted, and un-install them and re-install drivers.
If it is really bad, you may have to just start over and clean everything up and re-install Windows, and everything you had on your computer, but let's hope it does not come to that, because I think Windows 7 can fix most things if files got corrupted because of the mal-ware. Besides checking everything and un-installing drivers to basic-ly to get down to nothing again (driver wise and such) and re-installing, that is a start - well checking out what you can first of all.
 
You should have a anti-virus on your computer anyway, and there are free ones like Avira that work well. Better than some other ones.
 
 

Reinstalled drivers for Midi interface. Rebooted. Now The Input for port A is recognized, but not the output, and port B is not recognized at all. When I unplug the USB from the computer, Sonar recognizes an interface was unplugged and asks if I want to re-assign it. Tried different USB sockets, no difference.
 
The external box has lights indicating Midi signals going through it. When I play the keyboard, the port A light blinks now, but sometimes not. This keyboard is plugged directly into the Midi box, so I would assume the Windows drivers would have no effect on that functionality, right? Does this point to a failure of the box itself? I find that extremely suspect, coinciding exactly with my having had to take the computer in to have malware removed.

I went to the M-Audio website and found a KB article which solved the problem. I had to reinstall drivers again, but it turned out there were multiple instances of the drivers installed. I had to run a command line utility and then uninstall each instance before re-installing.

It's pretty often that you need to re-boot between each operation when uninstalling old and installing new.