Short Answer: Kaguya Otsutsuki was very powerful but her speed was just slightly above average. During her battle with Sasuke and Naruto, all she mainly did was hop from dimension to dimension, use a bunch of Kekkai Moras and absorb their attacks with her Rinnengan. Note that she is NOT faster than Raikage Ai when he uses the Lightning release chakra Mode to enhance his speed and reaction time. The only reason why Raikage could dodge it is cause he combined 2 Jutsus simultenously in order to detect and flicker away from the flames. Kaguya on the other hand, was not fast enough to dodge the flames. However, she was skilled enough to quickly absorb them before they did enough damage on her.
So to answer your question, the speed of Amaterasu was never increased, She just was not fast enough to dodge the flames like Raikage did.
Super Long explanation:
The Amaterasu is a very fast jutsu in terms of how long it takes before it is cast. Unlike other jutsu, all it requires is that you see the person you want to hit and then Black Flames are ignited at the focal point of the target! This means that as long as the user can see you, the Amaterasu is most likely going to hit. In order to dodge an "accurately-aimed" Amaterasu, I believe the persons speed must be pretty close to that of light because the focal point of vision is directly what your eyes see from the refraction of light. (Its a completely different scenario if the user is partially blind and can't aim well.)
In the case of Raikage, he used 2 jutsu's simultaneously in order to dodge sasukes Amaterasu. The first one is the lightning release chakra mode. During his battle with Sasuke, Raikage was wraped in lightning during the entire fight and once sasuke started to use the mangekyou Sharingan, Raikage instinctively started using way more chakra for the Lightning Release Chakra Mode in order to increase his already heightened speed and reaction time.
With enhanced speed and reaction time, Raikage was able to immediately react to sasuke's amaterasu, he then used the ShunShin no jutsu ( Lightning release Body Flicker technique ). Since he combined the 2 jutsus perfectly, he was able to instantly react to and swiftly move away from the flames (all within a matter of seconds, simply mindblowing lol). Moreover, Kaguya could not pull such a feat.