Transforming from abc reference frame to the qd0 variable reference frame?
You need the correct angle for a dq0 transformation to work. This is true for static velocity, constant velocity and variable velocity.

you say you have it working for constant velocity but not for variable does hint that you have not fully solved it for constant velocity since once you have the updated angle associated with constant velocity you actually have the solution for variable velocity.

What is velocity?  The rate of change of angle.
\$\omega = \dot\theta \$ 

so at zero velocity the angular position is static at some predetermined constant, the constant of integration. 

At constant velocity, the change of angle is a constant slope.  

Thus \$ \theta = \int \omega \Delta t \$.  

In short... find the integration block in simulink \$\frac{1}{s}\$ block with the input being velocity and the output being angle.