Electrical – Outlet appears to be switched but switches don’t work

It just seems like you have two 3-wire cables (with constant and switched hots) going into and out of that box, along with a 2-wire constant feed. It's not two circuits. The reds are switched and the blacks are constant hot.

IMO I would pigtail each color and use the side screws on the receptacle just like they were before.

That looks like #12 so you can no longer use the backstab/quickwire holes in the back of receptacles (in the US at least).

Some general rules.

1. Black and red wires shouldn't be going to neutral terminals. Silver is neutral.
2. In general, the tabs on the neutral (silver) side shouldn't be broken unless the upper and lower portions of the socket are being fed from different circuits.
3. Cable that has black/white/ground is called 2 wire (as in 14/2; the ground is not counted), and black/white/red/ground is called 3 wire (e.g. 12/3)

It sounds as if line power is coming into outlet box 2, the black/white cable. You can confirm that by turning off the power, disconnecting the black wire and leaving it clear of the outlets and other wires, then turning on the power and carefully checking to see if it is hot. Then turn the power back off before proceeding.

I would start with new outlets with tabs intact. (They are cheap). Break off the tabs on the brass side only on each.

Box 2: Connect the black hot (from the 2 wire cable) to the black from the three wire cable and to a pigtail (a short piece of black wire) with a wire nut or a push in connector. Connect the pigtail to the lower brass terminal. Connect the red wire to the upper brass terminal. Connect the two white wires to the silver terminals (the tab on the silver side should be intact).

Box 1: Connect both black wires from the three wire cables and a black pigtail with a wire nut or connector. Attach the black pigtail to the lower brass terminal. Connect the two red wires and a red pigtail with a nut or connector. Attach the other end of the pigtail to the upper brass terminal of the outlet. Attach the two white wires to the two silver terminals. (Tab intact.)

Switch box: Leave this as is, but cap the white wire if it is not already.

In all boxes, attach all of the ground wires and attach the ground to the outlet ground screw.

The lower halves of each outlet should now be always hot and the upper halves switched.