Did a search..... I just noticed that my front driver and passenger windows click while going up and down at about the same place on both windows, truck is 6 months old and I just noticed it.... It sounds like the track maybe?
Strange it does it on both.

 

That's Built Ford Tough for yah... Mine have chattered when opened 2" from day one of owning mine new... My GMs never did that, pretty annoying...

 

I wonder..... Mine were screeching pretty bad until I put some RainX on them last weekend in prep for the winter. Not saying this will fix it but i am curious is you have tried anything like that. May be an entirely different cause though. For me it was a lucky two for one.

 

Yea I will have the dealer look at it next oil change... sounds like the windows hit a cable or somthing during operation.