Hello,
I am trying to wire my ceiling fan light to two 3-way switches and my fan to a separate switch. I have the power source 14-2 running to the ceiling box, a 14-3 cable running from switch box 2, (3-way switch), to the ceiling box and another 14-3 cable running from the ceiling box to switch box 1, (3-way switch). I also have a 14-2 cable running from the ceiling box to Switch Box 1, (2-way switch).

I have the white wire from the supply cable 14-2 connected to the white wire of the ceiling fan/light combo fixture

I have the black wire from the supply cable 14-2 connected to the white wire of switch box 1 14-2 cable and connected to the 2-way switch.

I have the black wire from the switch box1 2-way 14-2 cable connected to the black wire of the ceiling fan/light combo fixture.

The white wires from the two 14-3 cables running from switch box1 3-way switch and switch box 2 3-way switch are connected together at the ceiling box and on the copper screws of the 3-way switches.

The black wires from the two 14-3 cables running from switch box1 3-way switch and switch box 2 3-way switch are connected together at the ceiling box and on the black screws of the 3-way switches.

The red wire from switch box 2 14-3 cable is connected to the blue light wire of the ceiling fan/light combo and is connected to the common screw of 3-way switch.

The red wire from switch box 1 14-3 cable is capped at both the switch side and the ceiling box side.

Then I have a jumper wire connected to the switch box 1 white wire 14-2 cable to the common screw of the 3-way switch in switch box 1.

The problem is that if switch box 1 3-way switch is off; switch box 2 3-way switch will not turn on the light. If switch box 1 3-way is in the on position then switch box 2 3-way switch will turn the light on and off.

Remove the jumper wire.
Connect the white wires of the 3-wire cables together in the ceiling box.
Connect the red wires of the 3-wire cables together in the ceiling box.
Connect the black wire of one 3-wire cable to the hot in the ceiling box.
Connect the black wire of the other 3-wire cable to the fan light wire.
Connect the black wire in each 3-way switch box to the common screw.
Connect the red and white wires to traveler screws of each 3-way switch.
The common screw is the black or darker screw.

Wow, looking at all this wiring here gave me a headache.

Harold, I'm going to assume your instructions are correct. If they don't work, OP, let us know, and I will take a closer look. But Harold should have you covered!