Here's my Tracker info (I accidentally screwed up the database mid-April and had to restart it, so without loading all of the historical turns again I can't go back farther than May 1 for HI cost. Can do so later but this seems sufficient to demonstrate that there's a problem, although not exactly when it started).

What I did:
After testing it in my AI game, and feeling that I will need the boost to make up for some blunders as well as what I perceive to be the "like attacking a rock wall" nature of my opponent, I decided I would clear out the top level of my flight schools to save a little bit on my pilot HI costs. This is a scenario 2 game, so they already start on the high side (at the time I was running a scenario 1 as Japan in tandem with this one, and its February '42 pilot costs were still 2/3 of what the December '41 Scen 2 pilot HI costs were).
At the end of March, I pulled all of my pilots from Replacements into General Reserve. Then I drew some pilots from the top level of my flight schools without touching the second level - my reasoning was that the top level didn't have terrible Exp levels (27-28) and it was acceptable to train pilots from that level instead of 40 Exp, while training from the second-highest School Level (17-18) was not worth it. I would rather pay the HI to get them to 27-28. So this was looking to save me ~6-7k per month for now, in return for a crapload of clicking on my end.
At the end of April, I emptied the top "quartile" of the pilot schools.
At the end of May, I only emptied the top quartile of one of the services but not the other.
I see this in the beta patch notes for 1123, from 20/01/2013:
"Pilot training HI expenditure not set in some cases"
Well, we started the game under 1123r or something like that, in early September 2013. I was getting charged HI for the first several months of the war. In March, I have written that I was charged -12361 HI.



