If the store is reputable and IWC serviced the watch and provided their two year warranty, I would be comfortable in the purchase as long as I received verification of the service by IWC.
While the timing should be better, such a condition can be caused by a variety of reasons, and it may have even originally escaped Schaffhausen with the issue. Even brand new watches sometimes have issues.
A brand new CF3 was placed in my hands for the first time at the Schaffhausen Boutique adjacent to the IWC Headquarters. And yet, upon arriving home I quickly found that the chrono minute counter did not work at all.
IWC of course was extremely apologetic and fixed the watch promptly. I'm wearing mine today in fact.
Issues like these shouldn't happen, but they sometimes do. One mark of a good company is not how they behave when all is good, but how they react when there is a problem. In my case, IWC reacted in an outstanding manner. The watch has been outstanding - I'm wearing it today in fact.
So with proper verification of the service, don't worry about why it needed service so soon. Relax knowing that you are covered by a warranty from a very fine company and enjoy one of the coolest watches to come down the pike.