I'm having this problem, too. I only started noticing it after I'd installed the beta freeplay release. My husband plays this too and hasn't opted for the beta, but he's been busy and hasn't been able to play since then either - so I haven't been able to test if it's actually related.
The problem I'm having is if I disable defending (like I like to do for my workers), and switch to a different group to give them a direction, then switch back to the worker group, both options are then disabled. I'm not tabbing out of the game at all. I've bound the group selection to keys on my mouse, so I thought maybe a keybinding for enabling/disabling food gather had gotten messed up and was also being triggered by the use of my mouse-key for group 1. I went into options and changed the food-gather binding to an obscure key I'd never hit, but the problem remains.
And the bug isn't play mode specific - I've encountered it in the main formicarium, in challenges, and in freeplay.
So far, that's all I've learned and can share about it.