Did more digging and I found what I think are the problems. No idea how it is to get fixed, but at least I have a way, with evidence to support my position. You might want to run some checks on symbols and see what shows up for you. This is using the TradeManager, not the analyzer and on the TS website Gain/Loss section.
Using the Orders and Average Price sections in the trade manager, I filtered 1 symbol for my entire time trading at TS and retrieved the information. I found several things for symbols I am having accounting issues with.
1. In other than the TradeManager, TS shows me flat a stock that I previously traded, which is correct. TradeManager does not. As an example in TradeManager I show having having bought a total of, 16,777 of DSS shares and having sold 16,786 shares. Not the case. As I said I am flat.
2. While the shares bought and sold for AAPL agree and the filled prices match my trading log, the P/L in the gain/loss center is off when compared to calculated dollar amounts using TradeManager.
The above were minor examples. I have a stock that I am flat on that shows I am long more than 1,000 shares. having traded more than 100 symbols, this is going to add up.