1. 3300 uF 3.60 nA
2. 3300 uF 2.78 nA
3. 2200 uF 0.63 nA
4. 2200 uF 0.19 nA
5. 2200 uF 0.04 nA
6. 2200 uF 0.25 nA
7. 2200 uF 0.17 nA
8. 1000 uF 17.14 nA
9. 1000 uF 10.65 nA
10. 1000 uF 37.22 nA
11. 1000 uF 14.10 nA
12. 1000 uF 12.54 nA
The TP340 24h stability spec @10V is 3mV and the temp coefficient is 2.3mV/C. Given the 3300uF/1Mohm time constant is nearly 1 hour, it is very difficult, if not impossible to make accurate sub nA leakage current measurments with this setup - 1mV of change in the power supply voltage translates to 1nA of apparent leakage current if the P/S voltage change occurs much quicker than the time constant.
DA makes it worse as the time constants are much longer. Every measurement will reflect the P/S ripple, drift and LF noise over the last hour or so. (I guess your meter will reject the 100/120Hz ripple and higher frequency noise when measuring the DC voltage across the 1Meg resistor). Your measurements are probably OK down to the nA level but not the 2 decimal points you show. A bit like measuring sea level rise by making spot measurements in the face of tides and waves.
The TP340 isn't bad but it would be much better to use a precision reference, even one of those dirt cheap AD584 ebay ones. Of course you could monitor the P/S voltage if you have a good enough meter to verify the P/S drift is not significant. Even then, ideally you would want to average the leakage current measurements over long periods - several hours at least, preferrably a day or more.
Alternatively, just open circuit the capacitors and measure the voltage every day for a few days, weeks or longer, but make each measurement as short as possible if your meter has 10M ohm input impedance, especially for the smaller capacitors - or compensate by estimating the charge lost during each measurement.
Don't forget to note the temperature as the electrolytic's leakage increases significantly with temperature. The change in dimensions of the capacitor with temperature will likely also change its voltage given that the plate spacing changes but the charge doesn't.
[EDIT] Added comment about P/S ripple.