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Only certain transactions not appearing

I sit down to budget every week or so and when I do I always check the final ending balance on Quicken to my bank statement. For 4 years it has worked, but I've been troubleshooting an issue for 3 days and I'm just about to call it quits with Quicken.

The USAA quick update changed recently and I didn't have any issues. I'm running 1 USAA checking account off the app and it's worked since that update for about 2 months.
When I sat down a couple days ago I noticed my ending balance higher than my online. When I started to get into the issue it just kept getting worse.

I reconciled with online balance and nothing was flagged. I went into the online center and nothing was flagged. I reconciled on my paper statement, which came out end of last week and still Quicken still didn't see anything. I reset my account and that didn't help either. After going through line by line for 2 months I found 4 random transactions that didn't make it into Quicken - some loan payments and a debit card transaction. My balance is still different by ~$300 now and it would be a waste of time to keep going back in time hoping to find the differences.

I created a new account and downloaded my transactions from USAA in and it brought those "ghost" transactions listed above. I compared those 45 days to current Quicken file and couldn't find any discrepancies beyond those 4 above transactions.

I'm curious as to why those transactions were not brought in, when there have been no issues for years. But now there's some huge problem

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