strange thing with nissan titan windows

I've never heard of them acting that way - you shouldn't need a resistor.  Those windows have no way to know where their position is (they should only have an "up" limit switch). 

What happens if you lower the windows all the way down and then short the wire directly to ground (bypass the relay)?  I've never tried to control the windows with a relay, just a straight ground.  It's possible (although not likely) that the contacts in the relay are bouncing enough to trip the anti pinch circuitry.

The door cylinder has three wires on it - a ground, a lock, and an unlock.  When you turn the key in one direction it connects either the lock or unlock directly to ground.  That ground signal is sent to the processor in the door (the power window controller).  The processor in the drivers door communicates through the BCM to a processor in the passenger door (this is all on a serial link). 

There are no double pulses or anything, those are only on Honda/Acuras!

No, there is nothing else to it.  What year is the Titan?  I can post pictures (or a link) to the service manual that shows the entire circuit.  The only limit switch the system uses is fully closed.  There must be something on your control side that is making it not work.

Try going with just the (-) output and eliminate the relay.  Also, try to just short it directly to ground and see what happens.  I really think you will find that somehow the relay is messing things up.

I thought you said you didn't notice the problem when just using the (-) output, I must have misread what you were saying.

Check out page 30 of the following PDF: http://www.nicoclub.com/FSM/titan/2004/gw.pdf

That is the window system.  Page 32 actually has the key cylinder on it showing you that it is just a ground connection

Page 33 shows the actual antipinch junk.  There is one limit switch that is closed when the window is fully closed and is open in any other position.  The anti pinch system on these Nissans works by the window motor turning an encoder.  The encoder then sends pulses back to a processor.  The processor can measure the frequency (tach) of the encoder and then calculate how fast the window is moving.  If the window is not moving fast enough the processor will stop the window and reverse its operation like the Titan is doing.  For some reason it thinks it is hitting something, which is why I said maybe the relay was bouncing a bit causing it to rapidly start and stop the window motor.  You may also want to try greasing the window tracks inside the door - that may help.