Q: Why didn't all of my files migrate to my new iMac while using Time Machine?

The files most likely transferred over, but the Dock shortcuts are not connected to them.

Try removing those shortcuts from the Dock and replace them with new ones from your Applications folder.

You're welcome!

For more info on moving Apps and using the OS X Dock

check out > Mac Basics: The Dock holds your favorite apps, documents, and more - Apple Support

and > http://www.macworld.co.uk/how-to/mac-software/tips-mac-os-x-dock-delete-apps-352 6992/

If that does not help...? Then perhaps you now have multiple user accounts and are not logged into the original one that was transferred over from the MacBook.

Lazorkat wrote:

 

How would I know if I have multiple user accounts?

Go to: Apple > System Preferences > Users & Groups and check.

I have a feeling that is the problem but don't know how to sync the accounts.

Depends on how you migrated the MacBook account to the new iMac.

(sounds like maybe you used migration assistant after initially setting up the new iMac)

If you now have multiple accounts, see > How can I merge two users on my iMac?

If your MacBook has not been wiped and you want or need to start over,

see > Move your content to a new Mac - Apple Support

You're welcome!