What version did you upgrade from?
Symantec Endpoint Protection 11.0.6200 (RU6 MP2) can migrate seamlessly over the following:
11.0.6000.550 (RU6),
11.0.6005.562 (RU6a)
11.0.6100.645 (RU6MP1).
http://www.symantec.com/business/support/index?page=content&id=TECH145428&actp=search&viewlocale=en_US&searchid=1294938757629