Nothing else in the box? Just the black/white/ground?

What kind of bulbs are you using? Did you switch from incandescent to CFLs perhaps?

Nope, black/white/ground is it. I did switch bulbs - the old fixture had two incandescents and a CFL. New fixture has five LEDs.

Did the three way work before it was fixed?

Yes, it worked fine before I switched the fixture.

Are there other wires in the box on which the fixture is mounted? If so, a connection/splice of one of those conductors could have been disturbed while swapping the fixture.
Granted that splices are supposed to be sturdy enough to withstand such handling, not all are done well enough to meet that standard.

There are no other wires in the ceiling box in which the new fixture is mounted.

If there was truly just those wires in the box the the 3-way either never worked right or one of the switches went bad, most likely it was the dimmer. And just so you know on a 3-way system it doesn't matter which way the switch is; up or down has nothing to do with on or off

So you used to dim CFLs? Is that dimmer rated for CFLs? Rated for LEDs?