You have to give more details about that because I don't get what you mean.
The timer can disappear, if you are kicked from the queue. Some action have this effect (changing current company for example)
It also disappears if you don't accept the game : you are then kicked from the queue.
The old bug with "choose army" button which makes it disappear has been fixed with the last patch.
There seems to be a new issue which is, you don't receive the popup to accept a game. In this case, you could also not receive the information that you have been kicked and the timer goes on. Or you can receive it and it disappears (which seems to be your case).
I'm working on it, unfortunately I have actually no idea of the real origin, and it's not reproducible on my side. That's why I'm asking for every logs I can get.