Rusty, have you tried booting into "safe mode" and then while in safe mode running a full virus scan? You might consider downloading & using Kaspersky's free AV scanner. If it finds an infection you can then download a free 30 Day free fully functioning trial of "KAV" which should then remove or quarantine the offending virus/malware. Not trying to start a which is best Virus/malware program discussion here, as there are lots of highly ranked anti-virus programs, just recommending one I know and trust and have been using for over 10 years with excellent results.
http://www.kaspersky.com/free-virus-scan
TIP: In addition to having a separate drive for individual file back-up's you should also consider doing separate "full disk image" backups every month or so using another external drive, or another partition on your existing external backup drive if it is large enough. That way, if you get hit with an unrecoverable virus/ransom-ware you can restore an image copy which overwrites your entire disk's OS, programs, files and all and you are then restored back to the date of your last full disk image backup.
Now back on topic...