I have been in the process of migrating Mailboxes from an Exchange 2003 enviroment to Exchange 2010, during the migration some of my mailboxes have been coming over as linked mailboxes and not users mailboxes. Here is an easy fix incase you ever hit this issue.
The reason it is showing as a Linked Mailbox is because the LinkedMasterAcount is set’
- Open up the EMS as Administrator
- To see the LinkedMasterAccount run this command “Get-User -Identity “user” | FL LinkedMasterAccount
- Run the following command “Set-User -Identity “user” -LinkedMasterAccount $null” This command will not have any output, but it will set the LinkedMasterAccount to null
- To verify run the same Get-User command from above. I will be Blank, or should be.
The account will now show as a User Mailbox and not a Linked Mailbox. If you need to do more than one account this command does accepting pipeline input, you could also use the Import-CSV Cmdlet to use a CSV as Input. To find out more information on the command go HERE
The Cloud Eh!? 
Thank you very much for this hint! fixed some mailboxes after upgrading from CU3 to SP1
Excellent! Glad it helped.
Unfortunately Exchange 2013 says:
Set-User -Identity “user” -LinkedMasterAccount $null
Cannot validate argument on parameter ‘LinkedMasterAccount’. The argument is null. Supply a non-null argument and try the command again.
However you still can edit the user attributes with ADSIEdit directly:
delete the msExchMasterAccountSid
set msExchRecipientTypeDetails=1
enable the user account
A bit more difficult that single command, but works on any Exchange version.
For scripting you can use the ActiveDirectory module with these commands from a selected AD: folder
clear-itemproperty -filter “msExchRecipientTypeDetails=2” -path * -name msExchMasterAccountSid
set-itemproperty -filter “msExchRecipientTypeDetails=2” -path * -name msExchRecipientTypeDetails -Value 1