Been noticing crafts fail to finish as the items sent over the wireless connection tend to get voided. When it comes to AE, hung crafts return their materials when canceled. This isnt the case with AE2 Wireless, it just erases them.

Wireless transmitter doesn't deal with items at all, what it does is tell AE that point A is connected to point B and consumes some power.

It's likely something about your setup that makes those item disappear (or end up somewhere you don't expect) or a bug in AE itself.

Do you have anything fishy in your logs as it happens?

Also please try replacing the wireless connection with a QB and see if it still happens (since those 2 are nearly identical in how they work)