Capacitors in parallel going negative
It goes up to negative a few hundred mV. Why?


That is why series capacitors have bleed/balance resistors across them. A negative reading is a sign that weaker capacitors (less charge) are being reverse charged by stronger capacitors (more charge). The dielectrics are NOT exact from one capacitor to the next, especially high value supercaps.

Capacitors in parallel do not have this reverse-charge issue, but the leakage values of each capacitor add up. Intentional reverse charging >1 volt is NOT recommended, as it is normally part of 'destructive' testing. This can damage the dielectric beyond repair.

EDIT: The high value resistors are part of the problem. Since you have 2 banks of capacitors of the same capacitance per bank, a single series resistor to limit charge current is fine. Add a 100K resistor across each bank for charge balancing, A 1N4007 diode across each bank (white band to + of capacitors) will prevent a discharge imbalance, by acting as a bypass for the bank that discharges faster, until both banks have drained to zero volts.

The larger value resistor 'protects' capacitors much better than with lower value resistors, assuming both capacitors are of same value. Normally capacitors in parallel attempt to level their charge difference, but series resistors can change this effect. The capacitor with larger value resistor will discharge much slower, thus maintaining a higher voltage (at its own terminals) much longer. The large difference in resistor values negate any chance of charge balancing. The difference in capacitor values exacerbates the problem. Look at your capacitors as trying to be equal, then look at your resistor delta values as an upset to this self-balancing act.