I am working on animating custom Views for my Android app. I have accomplished this via Property Animations and calling invalidate() on the View in the onAnim
invalidate()
onAnim
It sounds like your draw loop UI thread is getting starved.
I'd use traceview to be sure that there aren't any methods blocking your draw calls. http://tools.android.com/tips/traceview
This should help you determine what's being invoked instead of the onDraw method.