Sometimes the reports in Calxa do not appear to agree with the connected Accounting file, this is usually because of them being filtered differently.
To be confident that all the data is sync'd correctly,
Run a Balance Sheet or Trial Balance
Use the Original Account tree in both Calxa and the accounting system.
Report on the whole organisation
If these reports balance, then review the filters that are being used:
Account Trees
Business Unit Trees
Date Selection
If you are reporting on a group of organisations, run the P&L Comparison Report to give you a column for each organisation which can make it easier to understand what makes up the total amount.