One time this happend to me and it was becaue I had defined a unique key column that was repeated on a few different lines. Has that happend here?
To debug this, I would recommend using the Mendix Debugger tool. You are able to connect a debugger to a free node, and if you do this you should be able to step through this process and find a situation where it is failing. I would recommend putting a conditional breakpoint on the import flow to look for the error case.
In a free node, you are able to view the application log and set the application log levels. In your home.mendix.com portal, go to your project, then go to the 'Environments' link under the deploy sub-heading in the menu on the left. Hit the 'Show Application Log' button to go to a page where you can set log levels. After you have run this import process, try setting all flat file log node levels to 'trace' and run it again. You may get some errors there.
If all of that isn't working, put a big fat data grid on a page to look at all the imported records. You could add a sequential ID to the flat file, then sort that grid by sequential ID and make the page size 200 or something. You will be able to discover pretty fast which records are missing, then you can use a conditional breakpoint in a debuggger for your free node to find out exactly why those records are failing.
thanks for the answer rob. the debugger doesn't let me step into the java action, so i can't actually see why its failing. when i look at the logs, they don't capture that level of detail.