These two staements seem to contradict each other:
"vent light comes on with 1 wall switch"
and
"second switch turned on ... vent light".

Also,' you just tell us the number of wires (2 and 3), not the color coding; that is important to know. Do you know which of these is the power source? How were the old wires connected? That is also a BIG clue to us as outsiders.

Is the new fan just a fan? Or a fan and light combo? Because just a fan shouldn't have 4 wires coming from it. How about the brand & model number of the unit?

I seem to have the same problem. I removed a very old vent,heater,light combo from my house and wanted to replace it with a light fan combo. it has the same setup as talked about before 2 black wires and 2 white wires I understand that part. The problem is I have 2 switches and two sets of romex wire coming from the switch box and going to the fixture. I have one hot wire that is red going to one switch and black wire going out of that switch into the fixture. For the other switch I have a 3 wire romex cable that has a black and a red wire going from the switch to the fixture the white is has a wire nut on it and also goes into the fixture. I want to be able to shut each part of the fan/light combo on and off individually. I wasnt able to tell what was going where at the time of removal because of the small space the wires were in and as far as the setup at the switch the people I bought the house from had wired the switches differently because the fan had went out in the old unit so they had it setup to use the light only.