Mn ion doping of CdSe and other semimagnetic quantum dot (QDs) alloys has been an area of active speculation for over a decade. We report evidence of Mn(II) doping of CdSe grown from a cubic single source precursor that is superparamagnetic (SPM) with a blocking temperature of 40 K following thermal annealing. Prior to thermal annealing the 4 nm Mn/CdSe (1 % Mn) QDs exhibit mainly paramagnetic behavior between 300 and 2 K, with a weak antiferromagnetic exchange. Following thermal annealing of the sample, high-temperature ferromagnetic exchange is observed in the magnetization data with the onset of an SPM phase at 40 K that exhibits a coercivity of 0.1 T at 2 K. The switching-on of SPM behavior is believed to be linked to ion migration with formation of (Se-Mn-Se-Mn-Se-Mn)(n) centers within the nanocrystal that exhibit coupled magnetic moments. Electron paramagnetic resonance (EPR) provides evidence of two distorted Td Mn core sites, a clustered site (dipolar broadened), and a localized Mn site (hyperfine-split). The ratio of the EPR signature for the dipolar broadened site increases following annealing and shows a hysteretic response around the blocking temperature. These observations suggest that thermal annealing results in enhanced cluster formation explaining the onset of the SPM phase in these nanoscale materials. Evidence of SPM behavior is evident in the field-dependent non-Langevin magnetization with a tangential loss in the ac-magnetic susceptibility and the Mydosh parameter (phi = 0.16).