The difference occurs because the venn command reports otus that are shared by the two groups, whereas the get.sharedseqs command reports otus that are unique to the two groups. For example if otu 1 contains sequences from groups a,b,c and d. The venn diagram would report it as shared between a and b, but the get.sharedseqs command would not report it because it also contains sequences from groups c and d.
To make get.sharedseqs more flexible we plan to remove the groups parameter and in it’s place added unique and shared. If you enter your groups under the unique parameter mothur will report otus that contain only sequences from the groups you enter. If you enter your groups under the shared parameter mothur will report otus that contain sequences from the groups you enter as well as sequences from other groups. If you do not enter any groups mothur reports the otus that are unique to all the groups in your groupfile. Look for this in version 1.8!