When using a Windows laptop, you might be stuck with a synaptic touchpad.
Those crappy drivers with their so-called virtual scrolling create a fake window below the cursor to display their custom scrolling icon.
That window interfere with the signal sent to the application under, and GTK for some reason can't detect that (most likely the devs don't care about us).
The result is being unable to scroll in popular GTK apps like Wireshark or Pidgin.
After playing with Spy++ and Procmon for some time, I found an interesting registry key that solved my problem.
This setting will disable the custom cursor when you scroll, effectively fixing the scrolling problem in GTK apps.
First you have to open regedit. Navigate to HKEY_LOCAL_MACHINE\SOFTWARE\Synaptics\SynTPEnh and create a new DWORD called UseScrollCursor with a value of 0.
Restart SynTPEh (or reboot).
Scrolling should work in GTK apps now, but you won't see the scrolling cursor anymore.
Update: If that does not work, you can try to run
taskkill /im SynTPEnh.exe
Thanks to pieter for that link!