Reactions of a glucuronic acid (GlcA) β-thioglycoside with cyclohexadione show initial formation of the two anticipated all-trans decalin-type O2,O3 and O3,O4 cyclohexane-1,2-diacetals (CDAs) along with an epimer of the main O2,O3 acetal. This trans-cis isomer is then interconverted leading to higher amounts of the two all-trans products. Isomerization studies indicate slow interconversion between the all-trans CDA acetals, with only one undergoing significant interconversion with the minor 2,3-diastereomer. Crystal structures of all three isomers are included. These findings are relevant to other uses of CDA protections where occurrence of apparently disfavored isomers may be occurring, along with interconversions between CDA isomers.