OK, this is just weird: I've got a game setup file for France, saved at version 1.02. When I load it, all eight French depots are on map (two in Lombardy, one each in Hanover, Holland, and Palatinate, and one each in the French cities of Soissons, Cherbourg, and La Rochelle. Yes, that's eight depots, folks.
So, during setup, I want to change this file and move the corps and depot from Soissons to Namur (one area away). Once I've deleted the depot, when I try to place it back on map, it claims I have no free depots.
Sure enough, if I click the "View Available Counters" button before and after, it shows "(France) Depots Left Unplaced: 0" both before AND after I remove the depot. I tried removing a couple of different depots, just to see, and yet, they all show the same symptom.
Now, I know that during the game itself, I've seen some odd issues with depots, but it's inconsistent. I've never been able to pin down whether France should have eight depots, or just seven like everybody else. Having some of them "under" corps counters makes the search difficult, so I've always assumed I was just missing one. But, now I'm not so sure any more. I think there may actually be a bug in this area. It may only have to do with the French, but I can't tell for sure. I suspect when you find the bug, you'll know whether it applies to other MPs as well or not.
This seems to be a problem in the modification of setups created under old versions. France should indeed have 8 depots, and you have 8 depots here; it's just that when you remove one it isn't put back into the pool. In fact, you can remove them all and it still says you have 0 depots. I also tried some of my old setups; if I had 2 depots remaining, then that's all I have, even if I remove some.