I have a legacy Flex 3 application which I upgraded to the Flex 4 SDK. Some of the files (which did not change) still reference the 2006 mx namespace, but some are new and reference the new libary mx namespace.
Are the components found in the namespace http://www.adobe.com/2006/mxml different than those in the namespace library://ns.adobe.com/flex/mx or are they mapped somehow to the same component library?
According to "ADOBE® FLEX® 4 Features and Migration Guide" http://help.adobe.com/en_US/Flex/4.0/FeaturesAndMigration/flex_4_features.pdf (if it still loads):
You can still use the 2006 namespace, but you cannot use Flex 4 features (such as the new components and layout schemes) with it.
Also see section "Namespaces and packages in Flex 4" here: http://www.adobe.com/devnet/flex/articles/flex3and4_differences.html
BTW, the article is a good starting point for migrating to SDK 4.
Hopefully that helps.