This appears to be a bug. I tested it on SP and this doesn't occur. I renamed a piece of redstone dust and it does not interact with a redstone mechanism in the same manner as a normal piece. The redstone circuit is a hidden redstone switch, which gets reset by a piston that pushes the block the redstone dust is placed on, dropping it in the process. It works as expected with a normal piece, however, with a renamed piece, the circuit seems to activate, but the piston that would push and drop the redstone dust doesn't activate. If I break the redstone dust afterwards, the piston then pushes the block up, but doesn't pull back the block.
Renaming items has always been a little tricky on the Empire, items lose some of their functionality when doing so. As mentioned in the example: an iron block loses it's functionality to be changed into iron ingots again. I don't know for sure nor from mind if something similar also applies to redstone dust, but it certainly wouldn't surprise me. And unfortunately resetting the name in an anvil also doesn't help (though I haven't tested that for a while, it's possible things changed over time). Generally speaking it's better not to rename items on EMC if you plan on interacting with them. Such as converting blocks into ingots and given your example redstone dust as well. However, when thinking about your issue I'm now also wondering if you build the entire machine yourself? Because sometimes block protection can also cause a bit of trouble there, especially if you build something together with others. So: one item (say a piston) which doesn't correctly interact with another item (a block for example) because it was placed by separate individuals, and all of a sudden block protection kicks in. I somewhat doubt this is the case here, but still wanted to mention it to rule out possible causes.
I did indeed build the entire mechanism with Build Mode, but I also tested the same mechanism on my res without Build Mode and got the same result. I assume it's the renaming the redstone dust that is causing it.
