This issue has been resolved in the latest version of Sage 50 Accounts.  You can upgrade using the download and install guide.

 NOTE: If you use the Audit Trail - Grouped import option, you'll need to follow the workaround below after upgrading. 

Or, you can follow the workaround below.

When importing transactions into Sage 50 Accounts v28.1, import files that include a zero-value transaction will not be imported.

NOTE: In earlier versions, only the zero-value transactions were excluded from the import. 

To resolve this issue, you need to remove zero-value transactions from the file before you import into Sage 50 Accounts.