Sadly this did not help, have been doing development for quite awhile so that is not the issue. It did work briefly then went away. Strange that not only are the tools menu missing the other ones further on such as Windows and Help are missing as well.
Might have something to do with remote desktop which does strange things at time in Dynamics. I guess a lot do not see this problem since they are probably are admin in the Active Directory security config as well as Dynamics admin. In the past working with reports has shown a similar problem where I can create and change but not deploy due to SSRS and Active Directory security.