What slot is ur LM in?
Because of lag etc, there could be a difference between when the round ACTUALLY ended and when it appears to end for you. So if you generate chakra at latter part of a turn, you might not see the generation until the round have already ended on the server side.
The thing is, normal attacks etc doesn't really generate much delay/lag on your side as compared to the server, what generates a lot of delay is animated mysteries and chase chains. That's probably why it's more prominent on turn 2 and onward as opposed to 1, because there is very little delays source in turn 1.
There are two things that makes the delay worse, in my experience, one is 2x and the other is Xserver (arena/masuri). 2x is actually 2x on server side, but usually cannot be rendered at more than 1.5x on the player side (exact speed depends on your hardware and connection), and thus delay builds up. Xserver... I guess it's due to the architecture, but I get more delay there on mystery casting than regular stuff.
Similarly, I use the chase-generator on wind main. My pos 1 mystery will cause chase chain and give me the chakra, however, even if I Q my pos 2 mystery in the middle of the chase when I get chakra MANUALLY, it will ALWAYS be after enemy pos 3/4 mystery that is Qed BEFORE the start of my pos 1 mystery. This is because a chase chain is actually almost instant on the server side, so the next action is "confirmed" long before the chase ends (and before I VISIBLY get the chakra, this might be due to my wind main is on the last couple links in the chain too). I get around this by using auto, if I expect the income, I'll just turn on auto right after casting the pos 1 mystery.