The actions you describe are correct. When the Nav returns to the initial timer screen it should show an orange clock icon next to "Timer 1" and the indication "On." It doesn't matter whether you set only a start time, only an end time or both times.
It sounds like a computer error. If turning the car off and back on then going through the same procedure doesn't work, take it to the dealer. There is a slight chance that the problem will clear if you disconnect the 12v battery for about 10 minutes. This has fixed error codes in the past but I have no information that indicates that it would work for this problem.
I am sure other more knowledgeable people will be posting soon.
On 2nd thought- on the far right, in the Timer screen, be sure that the light next to "Timer 1" is lit!
1st Capacity Bar loss 30k mi 16mo
2nd- 49k mi 25.5mo 51.5Ah
3rd- 73k mi 36.5mo 46.9Ah
4th- 86.5k mi 43mo 42.6Ah
5th- 101k mi 50.5mo 38.4Ah, end 36.1Ah
New Battery 9/28/15 104k mi 66.1Ah
1st- 160.5k mi 34mo 54Ah
2nd- 184.4k mi 53mo 49Ah