Ring deuteration via the SEAr mechanism, which is usually problem-free, is found to be troublesome with methylenedioxy substituent aromatics. We report a case where the deuteration not only partially fails at one of the ortho positions but also is completely prevented by a conformation dependent effect at the other o-position. Such selectivity discrepancies are important due to the widespread occurrence of methylenedioxy substituted natural products. Density functional theory calculations were used to elucidate the exchange reaction mechanism in 1,2-dialkoxybenzenes.