I think the reason this happens is the way armor is replenished compared to health.
Medkits give health over time to what the SET HP is for the player (can change depending on variables like lua scripts extending or adding more HP) whereas how we handle armor on our server is via an entity scripted to SET the armor value to 100 instead of increasing it back to max. If you have 400/500 armor and use a armor kit, it will set your armor to 100/500.
Essentially, its SETTING your armor value instead of ADDING to it.
A way around this could be to make an "armor recharging SWEP" that functions identical to the bacta kit. But it targets the armor value instead of the hp value.
I hope that makes sense. <3
With custom scripting, Im sure this could be remedied.