[Suicide Junkie]

Note that the healing effect will happen with shield regenerators.

Partial damage that has not destroyed a component yet can be healed, but destroyed components will not heal (unless its organic armor)

Say I have a ship that takes 50 damage internally, but loses no components, and then my regenerators boost my shields up to 100.

The partial damage is added to the strength of the next hit, which depletes the shields. There is no longer any partial damage, so the hull damage + partial damage goes down.

The new problem you are facing appears to be that the armor is pumping more shield power than it should.

Also note that when you hit the enemy with just enough to drop its shields, they didn't take damage.
Observe:
Shields: 31
Meson bLaster hit: 30 damage.
shields=> 31-30= 1 hitpoint.
Since shields are up, armor doesn't boost shields.

Next experiment:
Shields: 29
Hit: 30 damage
shields 29-30 = 0 plus 1 damage to spread to components.
Since shields are down, armor boosts shield power by 30.

Final Experiment:
Shields: 30
Hit: 30 damage
shields 30-30 = 0
Since shields are down armor boosts shield power by 30.

And no damage is ever taken.

The shields being boosted to 120+ is very bad. I could only see that happening if you shot a shield depleter at a shieldless ship, & the energy was sent into the shields via crystalline armor.