You are absolutely right Trevorton, some malware apps actively prevent your preinstalled anti malware program from running. In my opinion, a better anti malware program is SuperAntiMalware! I know the name sound very suspect for those who have not heard of it, but I have been using it in a professional capacity for a number of years and it's brilliant, previously I used MalwareBytes.
Another useful application on the site, is the Tech version of the Scanner, when you download it, it is saved with a nondescript filename and extension so as to prevent installed malware from allowing it to run. You can run from USB key or dump onto your desktop and run in safemode. SuperAntiSpyWare is worth a look for anyone needing to run a scan. And I do not work for or am in no way affiliated with them, just a bloody good tool.