The reason for this is two-fold. This can definitely happen if you didn't change the scoring settings for the Who Should I Start tool to match that of your league in My Playbook.
The other reason is that the pool of experts utilized in the Start/Sit Assistant is slightly different than what is utilized in the Who Should I Start tool. The Who Should I Start tool will solely use the expert rankings that have been submitted for the applicable positional rankings according to which players you are comparing, or more specifically what position they play.
The Sit/Start Assistant is only using rankings from experts who have also submitted QB, WR, RB, TE, flex, K and DEF rankings. This results in the starting expert pool for the Start/Sit Assistant being slightly smaller than that of the Who Should I Start tool by a few experts. If you choose your experts for both tools so that the same expert rankings are being used for each tool, then you'll notice that both tools will choose the same player to start.