The plugin allows for whitelisting certain items - diamonds, emeralds, and other select items used to be whitelisted on old scarlet and in theory were carried over to new scarlet. I know NoNiche was tweaking the list, but it sounded like the plugin may not have been honoring the list at that time.
Yeah I added quite a lengthy list of items to be ignored a long time ago, but it seems to be hit or miss as to whether or not it is working. Not sure what the issue is .-. I'll take a look at it if I get a chance.
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...