I find that the majority of problems with DNA ligation inefficiency
are due to ATP degradation in the reaction buffer. If in doubt order
new buffer and freeze in small aliquots. You can also order Pharmacia
ligase - you have to order separate 10mM ATP with it to add to the
reaction as required. You have to be fairly accurate with the amount
of ATP added as too much is as bad as too little.
I hope this is of help to you