The order of your datasets listed on the MERGE statement is critical with a match-merge process, where there are duplicate variable names in more than one file you are merging. The SAS-hosted documentation at the link below discusses, in detail, the topic of One-to-One Merging and provides a specific CAUTION on this topic and the behavior you observed.
Scott Barry
SBBWorks, Inc.
SAS 9.2 Language Reference: Concepts, Combining SAS Data Sets: Methods
http://support.sas.com/documentation/cdl/en/lrcon/61722/HTML/default/a001081414.htm