HKEY_LOCAL_MACHINE\SOFTWARE \Microsoft\ConfigMgr10\AdminUI\QueryProcessors
Add a DWORD value for ValueLimit and set it to a, for you appropriate value. (eg. decimal value 5000)
For 32bits ConfigMgr 2012 Consoles on 64bits go to the following registry key:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\ConfigMgr10\AdminUI\QueryProcessors
After adding and/or changing the value restart the ConfigMgr Console and you will see the updated value limit.
Source post: SCCM Query Builder results limited to 2000 | System Center Stuff (wordpress.com)Â