As of this week, we will temporarily remove support for Lync connectivity with Windows Live Messenger in Office 365 for professionals and small businesses (Plan P). This means that customers using Lync with Office 365 for professionals and small businesses will temporarily not be able to see presence, IM and make video calls with people using Messenger. They will, however, still be able to see presence, IM and make video calls with other Lync users inside and outside their organization.
The reason for this temporary change is that individuals using a vanity or custom domain (i.e. yourcompanyname.com) with both Office 365 and Messenger were unable to access their Messenger accounts. By temporarily disabling Lync-Messenger connectivity, those customers can continue to use their existing Messenger accounts.
Here is an example scenario: Steve is currently using his business e-mail, steve@contoso.com, as his Messenger ID. Steve’s company has purchased Office 365 for professionals and small businesses (Plan P), where Lync-Messenger connectivity is enabled by default. Once the administrator at the company associates the domain contoso.com with Office 365, Steve will no longer be able to access his Messenger account. When Lync-Messenger connectivity is disabled using the Office 365 control panel, Steve will be able to access his Messenger account again as usual.
In Office 365 for enterprises (Plan E), Lync-Messenger connectivity (also known as Public Internet Connectivity or PIC) is enabled but turned off by default. If you decide to enable connectivity, please notify your users that they will not be able to use their business e-mail to sign into their Messenger account. This only affects individuals using their business e-mail address to sign in to Messenger, and does not affect those using @hotmail.com or @live.com e-mail addresses with Messenger.
We are working to address this issue and re-enable support for Lync-Messenger connectivity in Office 365 for professionals and small businesses in the coming months. We apologize for any inconvenience this may cause in the interim.
My comments: Finally Microsoft is fixing it, but a couple of months to fix it… 
there were reports of this as a problem very early in the beta.
