The stress counter is only increasing by the last amount of the phobie level, it should increase by the sum of all levels increased.
I had a phobie that i had ignored for a while and it had 2 upgrades pending, 3 to 5. My stress was 98. If i had chosen to upgrade from 3 to 4, then my stress would increase to 102, then repeat 4 to 5, my stress would then be 107. I took the option to increase from 3 to 5 in 1 jump, but my stress only went to 103 (+5).
I didn’t have the upgrades waiting, nor the fears to pay, but you could be losing quite a bit more stress using this short cut. E.g. 1 to 10 in 1 step would lose you 44 stress levels ((9×9 + 9)/2 -1)