and is in the rulebook that you reshuffle at the end of the deck only.
Could you point me to this?[if possible]
What you are saying (only add drawn cards back to the deck and reshuffle when the event deck is exhausted) is definitely the way Phantom Leader on Vassal has you do things. I'm playing my current North Korea campaign this way.
It does seem that it would make a difference as to how likely you are to see a given card (and to the potential ratio of good to bad events).