The point of washing with the 5% sodium bicarbonate is to neutralize the acid catalyst you used in the reaction. You would put the two layers in a sep. funnel, and keep the organic layer. Drying with sodium sulfate afterword (or washing the organic layer with brine) just helps remove residual water.
Is the product supposed to be a solid (sorry, I did not read the paper you linked)? I'm guessing once you rotovap down to 30-50 mL you take an NMR and look for your desired product and see none? How do you monitor the reaction? If the reaction does not go to completion, I imagine the glycerol is going to go into the water layer, so if you do not keep the aqueous wash you will not recover that SM, and if you only have the starting ketone, I imagine it would be pretty volatile, and could be lost when you rotovap away the solvent, especially if it's benzene (how high are you heating while rotovap-ing?). Your desired product also has a MW of 272, is it possible you are losing it during rotovap-ing? I'm not sure that it would be a volatile compound, perhaps someone else would have insights, but I guess it could be possible, especially if you are removing benzene under vacuum at an elevated temperature.