Which version of Factorio are you running? The update I made was to make it compatible with factorio 0.17, it should not have affected the 0.16 version though so I would think you are on 0.17 now. On the other hand if you installed the update, and went back to 0.16, then it may be disabled, and you will have to update to the 0.16 version.
Otherwise, can you check what UPS you have the mod set for in the settings, and what UPS you are getting in game?
If it's not the same, try going into the mod settings with the game loaded, and there should be a checkbox for "Reset the UPS to 60". Check that, go back to the game for a second, then go back into settings and deactivate it again. That will force the mod to reset the game speed. The mod does not aggressively maintain the game speed, rather only if the target UPS is changed so that players that want to adjust the game speed themselves still can.
