|Microsoft's previous add-on minimal anti-virus program didn't interfere with anything else working properly, so that's probably the case for Microsoft's Windows Defender, but I don't know for sure. |
You often have problems when more than one anti-malware program is installed if more than one each has a resident module - a part than runs all the time in the background looking for suspicious activity - and for that reason it's strongly recommended you DO NOT have the resident module of more than one anti-malware program running at the same time.
It's recommended you disable ALL such resident anti-malware modules from running whenever you install software yourself, AND when any complicated software is installed automatically or manually - e.g. Vista SP1 or SP2 updates.
The free version of Malwarebytes has no resident module, but the paid version does. The free version updates itself only the first time you run it - after that you musi update it before every time you run a full scan with it.
AVG 9.x free and paid, Avast! free and paid, AdAware paid, SpyBot free and paid, all Norton (Symantec) products, Malwarebytes paid, Windows Defender, etc., have one or more resident module (Norton products may have more than one).
AdAware free, Malwarebytes free, have no resident module.
You can disable the resident module from running in the anti-malware programs settings in most of them, or in some. e.g. Norton products, you can disable them temporarily for a specified amount of time.
You usually have no problems at all when you run an online anti-malware scan without disabling the resident module(s) of the anti-malware program(s) you have installed in Windows.