I just downloaded the update, read the changelog and it said:
[#1896] Redstone engine tweaks (SpaceToad)

I don't know what tweaks were done and I don't see documentation anywhere but they're not working at all. By not working I mean that I have redstone engines powering my wooden fluid pipes and they're not extracting fluid after I break and replace them. The other ones that I didn't touch are now operating at super slow speed and, as I said, if I break and replace them they will not extract fluid from the wooden pipes even though they were working perfectly before 6.1.2.

Also, something weird I discovered: I can only get the redstone engines to work with levers. I was powering them with redstone torches before and I tried this after breaking and replacing an engine. With the redstone torch directly on it or powering the block next to it, the engine won't animate at all. If I place a switch on the back, the engine animates really slowly (no visible speeding up) and as above, does not seem to work with fluid extraction.

I placed a creative engine on the wooden fluid pipe with a switch on the back and it operates properly so it has to be an issue with the redstone engines.

OK, I messed with it again and the behavior gets even stranger. I have one redstone engine powering the wooden fluid pipe extracting from my refinery and it IS extracting fluid but not constantly. It appears like it sits there for several seconds and nothing gets extracted (the refinery is green and at maximum efficiency) then it sends out a pulse of fuel and resumes sitting there.

The other one powering the wooden fluid pipe from my oil tank is doing the same thing but the pulses at which it extracts oil seem to be spaced even longer inbetween. The oil pipe has visible room for oil, I click on the tank to see if anything is being removed and the volume isn't dropping at all, neither can I see any visible oil filling the pipe until it gets one of those "pulses".

As to powering them. The one I have on my oil tank pipe won't work with a redstone torch on the back but it does work with a lever. The other one on my refinery works now with a redstone torch right next to it (the engine is pointed straight up at the pipe). I can't figure this out.

The redstone engines not extracting fluid constantly was fixed in a later commit than the public 6.1.2 beta, it'll be in the next release. And can I have some screenshots of the cases where the redstone torch isn't working?

http://img.photobucket.com/albums/v218/ChainedDown/2014-10-20_194304_zps1be9efc0.png

I sat there for at least 2-3 minutes to make sure it wasn't just lagging but sure enough it sat there and did nothing. If I put a lever where the redstone torch is and flip it on, the engine will at least animate. The lever on the back method works for all other types of engines.

You were right, I don't know how I got that screwed up. I tried the redstone torch like that with every other engine and sure enough, none of them worked. I feel like a complete idiot now. I probably made a big assumption based on the derpy redstone engine and my bad framerate. /facepalm

Really? It shouldn't. That's a vanilla mechanic actually. Redstone torches power all blocks around them except the one they're sitting on, even when on the ground.

Try placing the engine facing down and put the torch on top, see if it powers (It shouldn't)

Can you show me an example of another engine being powered this way?

Levers, however, power all blocks around them, including the one they're on. So placing a lever should work fine.

No problem, just know that the energy issue will be solved in the next release :)

The energy issue is fixed in 6.1.3. The torch issue is vanilla Minecraft behaviour. Closing.