I have not looked at RamperPro, but thank you for the recommendation! You can bet I'll be checking it out today. I've been looking for something for a while now.
And yes, I'm sure this more than what the OP was asking for. If the OP is trying to do the transition from day to night by letting the camera make every adjustment except aperture, I think he's going to have a hard time. Well, not just that transition--even just shooting moving clouds during the day you might have fluctuations in light. Lots of variables in any situation really, which is why I think a lot of us are suggesting he try full manual before he assumes it's a problem with the camera.
On a side note, this year one of my goals is to do more time lapse--got my Rhino sliders and now I'm looking to add a motor. I was originally going to go with emotimo because that's what I am most familiar with, but lately I've been thinking I'm going to stick with Rhino's motors. However, if you have recommendations for something else, let me know.