Okay, so, good news.
I did an update to my custom modpack for my server on friday that included updates to a handfull of mods, the most relevant to this issue being:
Forge: Updated to 6.6.0 build 497
IC2: Updated to 1.112.192-lf
APM: Updated to that testing version you recently posted in this thread.
And none of our benches have lost charge! Neither have they been eating items, so the issue seems to be fixed So thanks for that.
I don't know what exactly fixed the issue, but something in that update did.
However, I have noticed a lot of new issues since the update. For one, chunks are loading much slower than before (probably not the fault of APM), and I have been experiencing some pretty severe lockups (the server locks up to a point where it won't even respond to a SIGINT, and I have to send a SIGKILL to actually stop it). Again, I'm not sure if it is APM causing these issues because I am not getting any error logs at the time of these crashes.
So, I've been thinking of running a test version of my server with just APM downgraded to the released version and see if the problem comes back.