Can confirm that phases ship bullet time effect is not disabled when pressing B. Which is weird because in my last playthrough, I do not have this issues.
One odd thing I remember, I think, is the message that pops up when pressing B. Last I remember before my current playthrough, the message is something about bullet time being disabled, while my current playthrough its something about bullet time effect being 100%.
The Speedup function still work as normal, just the bullet-time isn't working properly. Sometimes though, even without the 2x speedup, pressing B while in a phase ship would cause the game to speedup even more than the 2x.
Below is my mod list, I don't believe any of these would do affect this mod functionality, by listing it anyway just in case.
enabled mods
{"enabledMods": [
"chatter",
"demandIndicators",
"DetailedCombatResults",
"fleethistory",
"fleet_journal",
"sun_flux_reticle",
"largerZoomOut",
"lw_lazylib",
"leadingPip",
"logisticsNotifications",
"lunalib",
"MagicLib",
"Marvelous-Personas",
"MoreBarMissions",
"MoreMilitaryMissions",
"more_procgen_names",
"more_ship_names",
"officerExtension",
"pt_qolpack",
"sun_ruthless_sector",
"speedUp",
"timid_tmi",
"WEAPONARCS",
"Rouge_Redstar"
]}