This is normal. You have to use up all your multi-battle attempts before reset. If reset time hits while you're at it, your multi-battles will then start using up the multi-battles on the current day. 

Also, I think the game is not supposed to be run in the background that's why it's slowing down. Mine even stops altogether if my phone screen gets locked. 

Someone pointed out the issue to me:

I have a Samsung S8 that was running with "game booster" which has an option to go into power saving mode when the screen locks. It still runs the game, but at a much slower rate. I turned that off and it runs normally even when the screen turns off. Saves battery by dimming the screen and "locking" it, but not as much as if it were to slow down. I'm okay with that since most of the time when I'm running multi-battle, I also have my phone plugged in lol