Had a little look and changed a few bits for you to go over. The problems you were facing were due to the layouts using the same event sheet, even though you added a new event sheets, you didn't change which event sheet the layout should use.
Changed the first event sheet and named it Engine. This is what will be powering the game. Include this on your level event sheets.
Also changed the way your setting the remaining critters and viruses. Simply added the number of each to update every tick. This way the games not relying on an action to update the remaining scores.
Also removed a couple of the virus total = 0 conditions as they were not needed. Game looks like a nice little project! Hope this quick revision helps.