Here are some ideas…others may have insight, too…
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As a rule, you should split manual transactions only after the un-split sources are reconciled. (Not sure how a portion of a split transaction was reconciled. You may have mismatched a portion of a split with another cleared transaction.)
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I have had this issue when I don’t put the correct account in the manual transaction dialogue.
(Was it checking or my credit card?) Sometimes, I may enter the transaction as a deposit when it is really a withdrawal. So it hangs out there reconciled, but cleared at the bank or my credit card statement, until I find the problem in my sheet (Then, I just delete the data in the Metadata column to keep this transaction from appearing in the options list for matching.) (If it was a withrawal instead of a deposit or vice verse, be sure to change the amount in your sheet, too.
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Amazon…Watch the matching of transactions carefully and skip those that aren’t exactly the same.
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Un-reconciled manual transactions will have data in the Metadata column on the Transaction sheet that look like this: “{“manualTransaction”:{“reconcile”:true,“ignoredIds”:}}.” After these are reconciled, these data are removed. You can sort your sheet by the Metadata column to see where your un-reconciled transactions are. (I use conditional formatting to shade these rows so I can see them more easily.)
Does that help?