RuggedCircuits, is the self-discharging due to air?
No, it's due to internal leakage.
The diode thing is interesting -- remember that it's a ~0.7V drop (~0.3V for a Schottky) as long as the diode is "sufficiently biased" with current, but as the capacitor nears full charge, it draws less and less current until the current is so low the diode voltage begins to approach 0! So I wouldn't worry about that too much.
A high ESR is actually a good thing for a battery-backup application. It limits inrush current (really, you do NOT want to load down your circuit with charging a 0.22F capacitance through nearly-0 ohms!) and the current draw out of the cap when it's backing up the RTC is so tiny that any series resistance causes negligible voltage drop.
The Gadget Shield
: accelerometer, RGB LED, IR transmit/receive, speaker, microphone, light sensor, potentiometer, pushbuttons