I'm obviously not sure in this case, but when it comes to input filters malfunctioning, in 99% of the cases it's a typo in the input file.
I'd say double-check the items you've added (maybe add them chunk by chunk, and see if smaller lists work), and make sure they all still exist (if memory serves, more than a few item codes changed in 1.13).
If importing one specific item code results in an error, I'm not sure the plugin is smart enough to output it legibly...
Good luck!
- Nev