Can the behavior be reproduced on Playback if you download a day of ES 12-19 data from the NinjaTrader Market Replay Servers?
With Immediately submit selected without the Synchronize account, would need the account manually synchronized to the position of the account. Other wise these will be out of sync.
However, I would not expect this to cause an exit order's total filled quantity to be different than the entry order's total filled quantity.
The issue looks like there was an execution from the last part fill that was not processed.
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