Really not sure why you would change this, as it has indeed been in the game since the elytra was introduced. Even if it was indeed a bug when 1.9 was released, the fact that it has been this way and you haven't fixed it for almost four years means that it's more or less become a feature. I know I use this frequently to allow flying downwards in 1-block columns rather than slowly climbing all the way down. It doesn't seem to break anything or allow any other problematic behaviors, so it seems far better to keep it as it has been.
I am experiencing this too, with a USB keyboard and Debian testing on kernel 5.3. I understand Linux is not a large user base, but frankly it seems like it would be hard not to catch a significant bug like this with even minimal testing. I hope someone can resolve this (I guess more likely to be the GLFW maintainers than Mojang), because the workaround is a bit of a pain.
I have encountered the same behavior. When moving away from certain bees, they stop moving when I get about 10 blocks away for more than a few seconds (how long is hard to measure with in-game tools, sorry). Their wings flap briefly, before freezing as well. This seems to happen to all bees which have been in contact with hives, nests, flowers, and have been bred by the player, however I haven't yet seen it happen with newly spawned bees from a spawn egg.
Contact with any other entity (including other un-frozen bees) makes them resume moving briefly, before freezing again as before. Going within 10 blocks of bees in this frozen state with a flower in either hand makes them resume normal behavior as well.
Here is entity data from bees in each state:
bee while fully frozen:
/summon minecraft:bee -44.82 131.80 241.99 {NoGravity: 1b, Brain: {memories: {}}, HurtByTimestamp: 0, FlowerPos: {X: -39, Y: 84, Z: 242}, HasStung: 0b, Attributes: [{Base: 10.0d, Name: "generic.maxHealth"}, {Base: 0.0d, Name: "generic.knockbackResistance"}, {Base: 0.30000001192092896d, Name: "generic.movementSpeed"}, {Base: 0.0d, Name: "generic.armor"}, {Base: 0.0d, Name: "generic.armorToughness"}, {Base: 16.0d, Modifiers: [{UUIDMost: -7230590118419873231L, UUIDLeast: -8771545964165856279L, Amount: -0.057467406681150024d, Operation: 1, Name: "Random spawn bonus"}], Name: "generic.followRange"}, {Base: 0.0d, Name: "generic.attackKnockback"}, {Base: 0.6000000238418579d, Name: "generic.flyingSpeed"}, {Base: 2.0d, Name: "generic.attackDamage"}], Invulnerable: 0b, FallFlying: 0b, ForcedAge: 0, LoveCauseLeast: -8619228188265336982L, PortalCooldown: 0, AbsorptionAmount: 0.0f, FallDistance: 0.0f, InLove: 0, DeathTime: 0s, HandDropChances: [0.085f, 0.085f], CannotEnterHiveTicks: 0, PersistenceRequired: 0b, Age: 0, TicksSincePollination: 13314, Anger: 0, Motion: [0.0d, 0.0d, 0.0d], Health: 10.0f, HurtBy: "", HasNectar: 0b, LeftHanded: 0b, Air: 300s, OnGround: 0b, LoveCauseMost: 3707801596262960063L, Rotation: [277.48062f, 0.0f], HandItems: [{}, {}], ArmorDropChances: [0.085f, 0.085f, 0.085f, 0.085f], Fire: -1s, ArmorItems: [{}, {}, {}, {}], CropsGrownSincePollination: 0, CanPickUpLoot: 0b, HurtTime: 0s, HivePos: {X: -30, Y: 81, Z: 243}}
bee unfrozen by proximity to flower:
/summon minecraft:bee -45.97 127.70 242.70 {NoGravity: 1b, Brain: {memories: {}}, HurtByTimestamp: 0, FlowerPos: {X: -39, Y: 84, Z: 242}, HasStung: 0b, Attributes: [{Base: 10.0d, Name: "generic.maxHealth"}, {Base: 0.0d, Name: "generic.knockbackResistance"}, {Base: 0.30000001192092896d, Name: "generic.movementSpeed"}, {Base: 0.0d, Name: "generic.armor"}, {Base: 0.0d, Name: "generic.armorToughness"}, {Base: 16.0d, Modifiers: [{UUIDMost: -7230590118419873231L, UUIDLeast: -8771545964165856279L, Amount: -0.057467406681150024d, Operation: 1, Name: "Random spawn bonus"}], Name: "generic.followRange"}, {Base: 0.0d, Name: "generic.attackKnockback"}, {Base: 0.6000000238418579d, Name: "generic.flyingSpeed"}, {Base: 2.0d, Name: "generic.attackDamage"}], Invulnerable: 0b, FallFlying: 0b, ForcedAge: 0, LoveCauseLeast: -8619228188265336982L, PortalCooldown: 0, AbsorptionAmount: 0.0f, FallDistance: 0.0f, InLove: 0, DeathTime: 0s, HandDropChances: [0.085f, 0.085f], CannotEnterHiveTicks: 0, PersistenceRequired: 0b, Age: 0, TicksSincePollination: 13848, Anger: 0, Motion: [-0.06521457611299691d, -0.006764298418545248d, 0.07642133858908207d], Health: 10.0f, HurtBy: "", HasNectar: 0b, LeftHanded: 0b, Air: 300s, OnGround: 0b, LoveCauseMost: 3707801596262960063L, Rotation: [285.60947f, -10.880027f], HandItems: [{}, {}], ArmorDropChances: [0.085f, 0.085f, 0.085f, 0.085f], Fire: -1s, ArmorItems: [{}, {}, {}, {}], CropsGrownSincePollination: 0, CanPickUpLoot: 0b, HurtTime: 0s, HivePos: {X: -30, Y: 81, Z: 243}}
a normal bee straight from a spawn egg which does not seem to be affected by this issue:
/summon minecraft:bee 35.85 84.15 242.72 {NoGravity: 1b, Brain: {memories: {}}, HurtByTimestamp: 0, FlowerPos: {X: 0, Y: 0, Z: 0}, HasStung: 0b, Attributes: [{Base: 10.0d, Name: "generic.maxHealth"}, {Base: 0.0d, Name: "generic.knockbackResistance"}, {Base: 0.30000001192092896d, Name: "generic.movementSpeed"}, {Base: 0.0d, Name: "generic.armor"}, {Base: 0.0d, Name: "generic.armorToughness"}, {Base: 16.0d, Modifiers: [{UUIDMost: -8403298993994316057L, UUIDLeast: -7859490514782730486L, Amount: -0.05443785083886528d, Operation: 1, Name: "Random spawn bonus"}], Name: "generic.followRange"}, {Base: 0.0d, Name: "generic.attackKnockback"}, {Base: 0.6000000238418579d, Name: "generic.flyingSpeed"}, {Base: 2.0d, Name: "generic.attackDamage"}], Invulnerable: 0b, FallFlying: 0b, ForcedAge: 0, PortalCooldown: 0, AbsorptionAmount: 0.0f, FallDistance: 0.0f, InLove: 0, DeathTime: 0s, HandDropChances: [0.085f, 0.085f], CannotEnterHiveTicks: 0, PersistenceRequired: 0b, Age: 0, TicksSincePollination: 394, Anger: 0, Motion: [0.0d, -0.004550229403953999d, 0.0d], Health: 10.0f, HurtBy: "", HasNectar: 0b, LeftHanded: 0b, Air: 300s, OnGround: 0b, Rotation: [318.75836f, -16.643373f], HandItems: [{}, {}], ArmorDropChances: [0.085f, 0.085f, 0.085f, 0.085f], Fire: -1s, ArmorItems: [{}, {}, {}, {}], CropsGrownSincePollination: 0, CanPickUpLoot: 0b, HurtTime: 0s, HivePos: {X: 0, Y: 0, Z: 0}}
Hope this helps, and if I have time I will set up more thorough test cases and try to help isolate a cause.
I also want to note that this is not related to the presence or absence of heart particles depending on graphics settings, and it also does not seem to be a performance-related issue. I have not had a chance to test other cases, but I observed this bug with axolotls spawned from a bucket-of-axolotls from the creative inventory. I will test later with spawn eggs and /summon to see if that makes any difference.