I believe Pixelmon 9.1.0 is using the gen6 speed tier calculation where it updates until the end of battle such as these scenarios:
How to replicate:
Turn 1 Mega evolve gardevoir against a target thats faster than it pre mega, but slower post mega (I tested with ninetales), the opposing pokemon will be faster this turn.
Turn 2 Your pokemon should be faster this turn.
Turn 1 Mega evolve venusaur against a ninetales, it should outspeed ninetales turn 1 due to chlorophylls speed boost still being active.
Turn 2 Your pokemon should be slower this turn.
Gen6 Interaction: https://replay.pokemonshowdown.com/gen61v1-1762539301
(What happens in pixelmon)
Gen7 and onwards: https://replay.pokemonshowdown.com/gen71v1-1762541078
(What should happen)