It seems that this commit in vte is related somehow:

commit 9f8c1b88dcd880c2d9e78c93521ee755560a9275
Author: Christian Persch <c...@gnome.org>
Date:   Mon Sep 30 23:00:09 2013 +0200

    emulation: Add support for DEC 1007 to set the alternate scroll mode
    
    By default, the mouse wheel sends cursor up/down keycodes in the
    alternate screen. This adds an escape sequence (DEC 1007) that allows
    turning this off (and on again).
    
    For compatibility with ubuntu's ******** patched vte, also add a
    (deprecated, skip) public API that has the expected name but does nothing.
    
    Based on patches from ubuntu, and Egmont Koblinger.
    
    https://bugzilla.gnome.org/show_bug.cgi?id=518405
    https://bugzilla.gnome.org/show_bug.cgi?id=709060

** Bug watch added: GNOME Bug Tracker #709060
   https://bugzilla.gnome.org/show_bug.cgi?id=709060

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https://bugs.launchpad.net/bugs/106995

Title:
  gnome-terminal unconditionally interprets mouse wheel events

Status in Gnome Virtual Terminal Emulator:
  Invalid
Status in xfce4-terminal:
  Confirmed
Status in screen package in Ubuntu:
  Invalid
Status in vte package in Ubuntu:
  Fix Released

Bug description:
  Binary package hint: gnome-terminal

  gnome-terminal started to translate mouse-wheel events into history
  scrolling, which doesn't work well when there's not a command prompt
  (another command running). this behaviour should at least be a
  configuration option; commands other than the shell may be confused by
  the escape codes sent as input.

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