I don't know if the valves being off would cause that issue or not. I am not saying it would or it wouldn't. But I think they would have to be off quite a bit to cause that problem.
How did you check for vacuum leaks?
The old school way to check for vacuum leaks it to use an unlit propane torch or carb cleaner. But this can be dangerous. I am not telling you to do this. But if you want to know, here is how it is done. Again, if you do this, be CAREFUL. http://www.popularmechanics.com/cars/how-to/maintenance/how-to-find-a-vacuum-leak-2
I prefer the torch method, outside of course.
If all the vacuum hoses are original, it might be a good idea to just go ahead replace them. Of course keep the originals.