Did you visualize your system yet? This kind of stuff has happened with me before. For me this happened due to the fact that a small part of the system got disturbed quite significantly because of some unwanted very close interactions which lead to high velocities locally and made the velocities of the rest of the system very very low. When the disturbance starts, the temperature increases drastically and as it decays down, the temperature keeps on decreasing and go far below the desired value.
In your case, this may happen as one of the sigma is one
See if this info helps you a little bit.