Seems you need to specify a unit to turn the CPT into a datestring cpt. I tried 1 hr and then the annotations worked better
gmt makecpt -Cjet -T2012-06-29T08:00:00/2013-10-18T11:00:00/1h > t.cpt
gmt colorbar -Ct.cpt -Dx4i/4i+w3i -B -pdf t
Seems you need to specify a unit to turn the CPT into a datestring cpt. I tried 1 hr and then the annotations worked better
gmt makecpt -Cjet -T2012-06-29T08:00:00/2013-10-18T11:00:00/1h > t.cpt
gmt colorbar -Ct.cpt -Dx4i/4i+w3i -B -pdf t