Hello Choo Choo Engineers!
Thanks to Wh00sh for bringing up this bug. If you had the Escape key assigned to quickly closing windows then even though a dialogue window such as the Upgrade menu or Scenario were open, on closing the Steam overlay the game would unpause but these dialogues would still be open.
The corrected behaviour is that when the Steam overlay is open, and the player presses the Escape key, if a dialogue window is open then the Steam overlay will close but the dialogue window underneath will stay open like expected and the game will remain paused like expected. If there is no open dialogue window underneath while the Steam overlay is open then when pressing the Escape key the Steam overlay will close and the game unpause which is the expected behaviour in that case.
Thanks for reporting bugs so that I can remove them!