There was a lot of loading and unloading going on, but I think the key problem was using the 'reload all'
In slot 5, there where roughly 30 raise charges, I used the reload all to switch to leveling charges, but there wasn't enough leveling charges to refill all 5 modules, so module 5 remained empty after the load all.
A while later, I went to switch back to raise charges, but they were all gone.
The same thing basically happened with the lower charges, which I tried to use because the raises had disappeared. used the 'load all' (it was hectic, wasn't trying to load all, but it's right next to load) and again, there wasn't enough lower charges to fill all 5, so some leveling charges were lost.
I 'think' that with the load all, if there's not enough charges, it doesn't unload properly.