Clear the XTickLabel before using datetick.. remove hold.. That should solve the problem..
y1 = rand(12,1);
y2 = rand(12,1);
startDate = datenum('01-01-2010');
endDate = datenum('12-31-2010');
time = linspace(startDate,endDate,12);
% time = linspace(1,12,12);
figure
% hold on
set(gca,'XTick',time, 'XMinorTick', 'on','XGrid','on')
[AX,H1,H2]=plotyy (time,y1,time,y2)
set(AX,'XTickLabel',[])
datetick('x','yyyy/mmm','keepticks')
EDIT This takes care of the ticks coming out wrong..
y1 = rand(12,1);
y2 = rand(12,1);
startDate = datenum('01-01-2010');
endDate = datenum('12-31-2010');
time = linspace(startDate,endDate,12);
% time = linspace(1,12,12);
figure
%hold on
[AX,H1,H2]=plotyy (time,y1,time,y2)
set(AX,'Xtick',[],'XTickLabel',[],'Xlim',[min(time) max(time)])
set(gca,'Xtick',time,'XGrid','on')
datetick('x','mmm','keepticks')
