Having the same problem.
I have all of my transactions split out into seperate spreadsheets per exchange. I've spent many hours getting these balanced out to zero.
If I delete all transactions from CoinTracking then import one of these sheets everything looks fine initially.
"Current Balance" on the dashboard, the "Current Balance" report, the "Balance by Exchange" report, and the summary at the bottom right of "Overview and Manual import" are all 0.00 as expected.
But as soon as I click "recalculate trades" everything goes haywire and starts telling me I have balances that I do not.
I wasn't having this problem last time I worked on this a week or so ago.
Manually adding a tiny transaction per coin seems to fix it but this isn't a solution.
Very frustrating!
got a response from support it was due to the server migration and should now be sorted