Thunder and lighting still occurs while the game is paused during the rain.
If you leave the game paused the light flash and sound from these effects still cycle. This occurs on both the esc menu (the one with save, load, new, quit and options) and in the inventory.
(RM-1706 from redmine: created on 2014-07-26 by Eh Kay, , closed on 2014-10-13 by Justin Sane)
Edited by redmine