Are the deuterated and non-deuterated reactions performed at the same scale?
Reactions done at small scale often have lower isolated yields. Let's assume that 250 mg of your product gets lost due to absorption on drying agent, filter paper, and other mechanical manipulations. If your scale is 10 g, then your limiting yield is 9.75 g (97.5%). But at 1 g, your yield is limited to 75%.
The differences you see between deuterated and nondeuterated may come down to that.
You usually see the 2° KIE when there is a change in geometry ("hybridization" if you think that way) of the atom with the D attached. This doesn't happen in your reaction - the D on the alkoxide is tetrahedral all the way through. If there was a KIE, it would slow the reaction down by a factor of about 1.2 - unless you are stopping the reaction too quickly, that won't change the yield.
If your reaction is under equilibrium control, there can be Equilibrium Isotope Effects. But these are unusual, and the shift in Keq to drop a yield from 90% to 60% would be unexpected.
If you are getting enough product to move forward with your research I wouldn't over analyze it.