In order to generate a file that contains your CheckBook or CheckBook Pro data, you'll want to use the Export options rather than the Import options. Unfortunately, though, CSV is not an available Export option, so perhaps you could try the tab-delimited Text format, which is pretty similar to CSV and can be opened in programs like Excel or Numbers as a spreadsheet. For that, choose Export > Text... from the File menu.
Alternately, if you are talking about importing a file that's been downloaded from your online bank in CSV form, then it's possible that the imports failing due to atypical formatting. In that event, it would be easiest for us to determine the root cause of the issue for sure if we could get a hold of your file in order to test with here. So, if you'd be willing to send that over to us, just attach it to an email to
support@splasm.com and we'll have a look. Thanks!