Yumil

This appears to be just another passing anecdote of this occuring through no intended feature. I think there's a couple reports about it in the proper forum section.

You might be happier with a more knowledgable reply, but I'll attempt to assist. I believe they can only junction on a special kind of Steve's Carts rails? I'd suggest investigating the available rails if you haven't yet. I'd be more help if I was home to do the guesswork for you but alas, work.

Sorry, my post was a ruse for some cheap laughs at the thought of "disabling" and replacing all dirt.

I disabled dirt, minium stones, and replaced all dirt with Basalt Paver. sorted Dirt is imba and forbidden.

According to the update note that Plowman pasted, it doesn't look like Redstone engine to conductive pipe functionality is wanted, but I'd assume the other engines that make MJ can send power through conductive pipes. I almost feel like this "work-around" with the Pneumatic Generators from IC2 Transformers addon is going against the desired functionality that the BuildCraft dude is going for but for now it works. If for some reason redstone engines are changed to stop working with the pneumatics even, then there's still BC Consumer->Energy Bridge->IC2 Producer blocks from PowerConverters. (Edit: But I'm actually not sure if redstone engines will give power directly to a BC Consumer, I might try later for the fun of it though it's crazy inefficient)

It's in some update notes that they'll no longer produce power into wood conductive pipes. But you could simply do something similar like you mentioned in your first post but using these newish items the pneumatic generators. My setup for some simple free power is redstone engines pumping directly into a "LV Pneumatic Generator" which takes in MJ and outputs EU, so from there you can plop your batbox next to it on the side that lacks a redstone engine, or you can cable it out. It's not so bad of a change. I enjoy anything that makes what used to be easier or more difficult, more hard to do. Now instead of being able to easily make huge arrays of these redstone engines going into pipes, you at least need to craft a pneumatic generator for each set of redstone engines. So you can do the same stuff, just takes more crafting resources.

You can still step cobble and other low worth rocks up into better forms of matter with the minium stone functioning just like the previous philosophers stone. You could effectively set up an automated process of upgrading cobble to your desired material, it just requires more effort now, which I hope is a theme that sticks around with EE3.