Background-- I had ground wires that were hooked up outside the box. I wanted to meet code during a renovation and put the ground wires in the box.

So... everything worked normally.

I disconnected everything, got the grounds back in the box.. all of the lights work... but they won't turn off at the switch.

So I guess I have the switch hooked up wrong at the box or the lights hooked up wrong at the box. Any ideas

You didn't do anything at the 2nd switch, correct? Does it turn the light on and off correctly? It would help if you could tell us the result for each of the 4 possible combinations of switch positions:

Switch 1 up, switch 2 up:
Switch 1 up, switch 2 down:
Switch 1 down, switch 2 up:
Switch 1 down, switch 2 down:

Remove all wires from switch. Separate them such that they do not touch anything. Turn power on. Mentally identify wires as 1, 2, and 3.

Very carefully touch wires 1 and 2 together. If light comes on either wire 1 or 2 is common. Touch 1 and 3 together, if light comes on wire 1 is common. If light does not come on, touch wire 3 and 2. If light comes on wire 3 is common.

If light does not come on when you touch wire 1 and 2 together, touch wire 1 and 3 together. If light comes on either wire 1 or 3 is common wire. Touch wire 1 and 2 together. If light comes on wire 1 is common wire. If light does not come on, touch wire 3 and 2 together. If light comes on, wire 3 is common wire.

If light does not come on when you touch wires 1 and 2 and does not come you touch wires 1 and 3, touch wires 2 and 3. Light should come on. If light comes on, either wire 2 or wire 3 is common wire. Touch wire 2 to wire 1, if light comes on wire 2 is common wire. If light does not come on, touch wire 3 to wire 1. If light comes on wire 3 is common wire.

That's all the possibilities.

After you have identified the common wire you should be able to touch the common wire to one of the other wires and have the light come on. You should then be able to flip the other switch and touch the common wire to the other wire and have the light come on.

Put the common wire under the dark colored screw (usually black). Put the other two wires under the other two screws, doesn't mater which wire goes under which screw.

OR

You can remove the other switch and see which wires are under the traveler screws (usually brass). Put those same wires under the traveler screws. Put the remaining wire under the common screw.

The quickest/fastest/easiest way to fix, that I have found is:
Remove wires from both 3 ways, now see which of the 6 wires is hot, hook that to the common of that 3 way switch, the other 2 wires to the 2 same colored screws(travellers).
Go to the other location and see which of the 3 wires is hot, hook that to a traveller screw, flip the other switch and see which of the 2 remaining wires is now hot. Hook that to the other traveller screw. You should have 1 remaining wire and that hooks to the 2nd 3 way switch common(that wire goes to your light).
Good Luck