One issue you
might have is a bad USB port or keyboard cable with a broken wire.
Generally I've found that if a USB port is bad that what ever device is attached through it will periodically just disappear. Windows will inform you of this saying that device abc has been disconnected. But if there is, for example, a broken transmit wire which losses contact periodically through minor--or larger--movement of the cable, when you press a key the signal created by pressing a key might just get garbled or lost and thus be ignored by the windows driver.
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Pocus said he was going to add something to display purchases made by auto-replacement. I think before that, any observations will be speculation at the very best.
Basically what you are observing is this:
A: [Conscript production - not seen by player] -> B: [auto-replacement purchases using some of the produced conscriripts - not seen by player] -> C: [conscripts available to player]
In this situation you are speculating that "C" is incorrect. Without knowing "B" to extrapolate "A" or having "A" presented directly, there is now way to make an informed opinion on whether "A" is too low or not.
I can suggest 2 productive things you might do under the current circumstances, both of them with AR turned off.
1) Run a couple of turns of a scenario--the best would be from the middle of a running scenario in the middle of summer--without issuing orders to either side--do not allow the AI to create orders--so that there is as little interaction between both sides as possible. Do this by loading first one side and clicking 'save orders' and then loading the other side to do the same. Then return to the side you are observing and execute the turn. Now check conscript production.
Do this for a couple of turns to see if production remains more or less stable and record the levels are.
2) Copy a saved scenario into a previous installation--you may have to reinstall an older version into a unique folder (I ALWAYS install into a folder name representing the installed version, for example "CivilWarII v1.05 RC7-PB 1 Test")--and do the same as in 1) using the exact same starting point. This will give you something with which you can compare.
I can heartily recommend using this method for making screenshots to record your observations:
How To Make Screenshots and Post them in a Thread