It seems that the recent barrage of changes in Google Analytics have given way to some loose ends. Since November 15, 2011 we have been seeing a large number of visits with the destination URL as (not set) within the Adwords report in Google Analytics. This bug is being seen across all our accounts. Other folks have been reporting this issue as well. We hope the good folks at Google can resolve this issue as soon as possible & provide the correct data for the affected period.
The screenshot below illustrates the data discrepancy being seen since Nov 15, 2011.