An issue that I recently came across was when we upgraded our servers from BizTalk 2006 to BizTalk 2006 R2 is that we were unable to see the new EDI features. This is the context menu I saw when right clicking the parties:

Which is incorrect, I should be seeing this context menu:

The resolution is that after you upgrade the server, you need to need to modify the installation in the add/remove programs and choose Modify:

Check the BizTalk EDI/AS2 Runtime:

Afterwards, you need to go into the BizTalk Configuration and configure the new EDI components (I already did this):

Then you get all of the components you are looking for.