I cannot recommend you accounting tool to count profit. Need to check what program work now. Without balance/day graph which count items, free isks, isks locked in orders etc. it is difficult to tell what is wrong or OK. I expect that trading as activity is less profitable now, because trading require activity on the market. Player's online dropped in the past couple of months due to null blackout and other reasons. What trade bot will earn if nobody will buy or sell? Nothing.
Online is returning, hopefully this is not just bots but real players.
If you send me log I will check if program works w/o problems. Also make sure you correctly set brokers fee and sales tax, as they recently changed.