Hi Hyde, I assume you selected your cells with puromycin following transduction with rtTA-puro, and then transduced the selected cell population with TRE-mCherry. Did you select your cells after second transduction? If not, then your results could be explained by the reason that some cells were not successfully transduced with TRE-mCherry. Otherwise, difference in the location of transgene integration can account for the heterogeneity you observed. Depending on the location, sometimes TRE promoter can be masked by promoter methylation or histone modifications, and therefore does not respond to Dox.
BTW, what cells did you use for your experiment? Also, what was the concentration of Dox?