Well, I should have counted to 10 and kept trying, but maybe this will help some one else out. The vertical size of the rect for the first slider was overlapping the bottom one. Here's the fix:

    // Initial Velocity
GUI.Label(Rect(3,300,200,50), "Initial Velocity");
velMagnitude = GUI.HorizontalSlider(Rect(3,320,200,20),velMagnitude,0.0,500.0);
GUI.Label(Rect(220,320,20,20), velMagnitude.ToString());

// New theta slider
GUI.Label(Rect(3,360,200,50), "Theta");
newTheta = GUI.HorizontalSlider(Rect(3,380,200,20),newTheta,0.0,90.0);
GUI.Label(Rect(220,380,20,20), newTheta.ToString());

where are you defining the variables "velMagnitude" and "newTheta"? it sounds like you may be defining velMagnitude in the class body, but newTheta only within the scope of the local function, so when the function ends it is forgotten and re-created afresh next time round (with the same initial value).