What is this manga about two students who speak to each other through a window?
I have been searching for this manga too and I hope it's the same manga you were searching for.

The name of the manga is Shuu 7. The manga consists of 4 one-shot stories and the story you are looking for is the third one.


  3) Koi no Kajitsu (Fruit of Love)
  
  Yuzuhara had to quit the track and field team due to an injury and is down because of that...then one day Tooda Shuuhei pops in at the window where she sits and asks her to date him...although shocked Yuzuhara agrees him to see at her window seat for a month until her seat changes...but on the last day before her seat changes Shuuhei doesn't turn up...