I don’t think you will like this idea very much but in fact because of the aforementioned¹ bug I got into the habit of checking on the stopwatch constantly² out of fear it would disappear.
So switch to iOS while the bug is still there 
On a more serious note: You could try to rely on the ticking sound of pomodoro apps. This way you have audible feedback that there is a timer running. Instead of measuring the time with the Beeminder app you’d measure the time with the pomodoro app happily ticking away and then enter your 25 minutes when it’s done. Of course that’s yet another tool in the box which needs clicking. But maybe for now that’s better than not having any data on how long you did something.
¹ I always wanted to use this word
² About every 15-20 minutes