When trying to put an item into the item responder chip filter (or any other chip with a filter) the item is not added to the filter and the item stack is entirely deleted. This makes the whole transportation system unusable.

Using: Minecraft 12.2, Project Red v92, Forge 2824

This issue is related to JEI:

When having the JEI Bookmarks open, the filter window will be behind the JEI window. This will cause items to be put into JEI instead of the chip crafting window.