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Still not sure why the original code didn't hit that if-statement. A type change and a memory leak later, I got it to work:

private void euclidChannels(Mat in, Mat out){       
    in.convertTo(rgbF, CvType.CV_32F);
    Core.pow(rgbF, 2, rgbF);
    rgbF = rgbF.reshape(1,rgbF.rows() * rgbF.cols());
    Core.reduce(rgbF, gF, 1, Core.REDUCE_SUM);          
    // fix rgbF - constant time
    rgbF = rgbF.reshape(3, in.rows());              
    gF = gF.reshape(1, this.height);            
    Core.sqrt(gF, gF);                  
    gF.convertTo(out, CvType.CV_8UC1);      
}

Re-reshaping the rgbF matrix back to it's original state was key to eliminating the memory leak, as apparently convertTo() will re-allocate the destination matrix if it doesn't like the one you provide. (I guess I could have added another temp matrix instead, but reshape() is supposed to be constant time, so might as well save a bit of memory)