In most cases, the metal enolate of esters are hydrolyzed during aqueous work up. You should check again the structure of by product carefully by spectroscopic methods.

As an additional information, the success and failure of reactions including carbanion species are sometimes depends on the order of additions of each reactant or reagent. As well as, investigate when that by product are formed.

A couple of years ago we used to prepare the lithium enolate of several acetate esters and one of the ways that helped us in avoiding self condensation was the use of LDA at -40.  You can use freshly prepared LDA or a titrated solution, it doesn´t really matter.  But you should make a slow addition of your ester to the LDA solution NOT BACKWARDS, once the enolate is formed (formation of a solid) you can add the second ester and you won´t have any problems... Hope this will help you!!!

As mentioned above, order of addition can be quite important, as can assessing the relative acidities. Difficulties are most commonly encountered if both esters have acidic alpha protons and sometimes the product acidity can be an issue. Depending on the esters used there are other options if the classic Claisen conditions fail.

keto enol tautomerism of your product may be complicating your isolation and characterisation due to rapid exchange of protons. I have found that the use of deuterated methanol as an NMR solvent can help resolve spectra to a single enol tautomer for characterisation purposes as any additional deuterium is easy to account for.

Kapse,

You may look at 

http://www.organic-chemistry.org/namedreactions/claisen-condensation.shtm

and gain more info 

Good luck

 Method for the Claisen condensation by reacting two moles of etyl acetate in presence of sodium ethoxide in dry etanol under reflexing condition & concentration to get desired acetoacetic ester.