If you are using MSMQ with BizTalk ,or just MSMQ in general, there is something that breaks in mq.sys. I have not found out exactly what it is but I do know there is a hotfix for it. Below is the link to get it.
Now I ran into this problem while logging onto the server. Consequently had to boot into safe mode with networking. Safe mode will not run the two MSMQ services and allow you to fix the problem. You can then apply the hotfix and start the services. Happy BizTalking!