In the real world, I wouldn't expect two capacitors to charge-up equally. There will be differences in capacitance, series resistance, and leakage resistance. Once the capacitors are fully-charged, the leakage resistance creates a votage divider for the applied charging voltage, and if the resistance isn't equal, you don't have equal voltage.
To do this properly, I think you should charge each capacitor separately to 2.5V (or 2.7V), and then connect them in series.