Erm, not really sure what a "good cook" is...
OK, so if I've got this straight, you are doing a reduction of an ester by dissolving the substrate in ethanol/water, and adding a solution of NaBH
4 in ethanol/water to it?
Using such solvent mixtures will often cause problems in work-up when dealing with relatively polar products, so it's not all that surprising that your product is split between phases - i think this is where the issue arises from.
Could you perhaps simply evaporate the ethanol/water from the vessel, then apply the residue to column chromatography?
Or maybe use neat THF or ethanol or methanol in place of the ethanol/water system? This should be easier to evaporate...
Or use DMF (can't remember bout the solubility off the top of my head though) as the solvent. If done on a small scale (say 1 or 2 mL of DMF), you might be able to apply this straight onto a column without bothering to work it up...
These may or may not work! I can't be held responsible if it cocks up !