Exchange Online user with Office 365 cannot send mail as only on behalf

You can try these commands for the Windows Azure Powershell
$LiveCred = Get-Credential

$Session = New-PSSession -ConfigurationName Microsoft.Exchange -ConnectionUri https://ps.outlook.com/powershell/ -Credential $LiveCred -Authentication Basic -AllowRedirection

Import-PSSession $Session

To verify that the permissions send mail on behalf of another user:
Get-Mailbox -identity user@example.com | fl *GrantSendOnBehalfTo

To remove Send On Behalf permission from a mailbox, use the following command:
Set-Mailbox -Identity user@example.com -GrantSendOnBehalfTo $NULL

As comfortjeanius suggested, you need to verify the permissions. It's easiest to do this using the EAC:

http://technet.microsoft.com/en-US/library/bb123809(v=exchg.150).aspx#MailboxDelegation

Ok user has send as and full permisson to the mailbox
She has it added under her mailbox and she can reply and change the from to the secondary mailbox  but when in it doesn't default to secondary.

Well the default one is configured by setting the default account in Account settings, it will not change based on the context. If this is a normal mailbox, she can add it as separate account in Outlook and it will auto-update the send address depending on which account she is working with (on Outlook 2013 at least).

If this is a shared mailbox however, the send from address will not change to it. As a workaround you can add the shared one as POP account so you can set it as the default, but again it's not an ideal solution.

To assign "Send on behalf of " permissions

Set-Mailbox -Identity <DisplayName A>  -GrantSendOnBehalfTo <DisplayName B>

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To remove "Send on behalf of" permissions

Set-Mailbox -Identity <DisplayName A> -GrantSendOnBehalfTo $null

Select allOpen in new window

Plus here is some information for your safe keeping Mailbox Permissions - PowerShell commands

@ comfortjeanius - she does not want to send on behalf, but send as

@ vasilcho - ok to clarify If I have my mailbox open in Outlook and a secondary with full access and send as.  If I am in the secondary mailbox under my account and reply it will NEVER send as that user as it is under my account?

I want to make sure I'm clear as I can just change the from field and it will work, but the user would like to avoid that step and told me it used to work so want to make sure I am clear it is not possible.

You nailed it thanks!