Issues with using contact reports due to the number of contacts in system

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We are finding it hard to use certain contact reports and believe it is due to the number of records we now have in our system. However, I have noticed that the issue has occurred after our last two upgrades. The last upgrade I was able to make some configuration setting changes but those setting are still where they were at prior to the upgrade to February /16. Each morning I come in the report we use is set to "set report to deferred execution" and I have to uncheck it. It is good for the day but to have to