Even the cobble cycle is OP compared to other conversion devices meant to convert MJ's into EU's. especially with the thermal generators added by gregtech. (OP because it's a loss-less conversion while all other systems incur rather big losses, and that is how it should be. there should be a cost incurred when basing your energy production on only one system)
I don't see where you're getting a loss-less conversion from the cobble cycle. Looking at fuel values, most basic fuels that can be burned for either MJ or EU give 2.5 times as many EU as MJ.
Coal/charcoal: 4k EU/1.6k MJ = 2.5 EU/MJ
Wood/planks: 750 EU/300 MJ = 2.5 EU/MJ
Sticks/saplings: 250 EU/100 MJ = 2.5 EU/MJ
Peat: 5k EU/2k MJ = 2.5 EU/MJ
Bituminous peat: 10.5k EU/4.2k MJ = 2.5 EU/MJ
Cobble -> Lava costs 20k MJ (burning the same fuel to get EU directly would typically get you 50k EU). Putting that through a geothermal generator gives you 20k EU, a 40% efficient conversion. The thermal generator improves that to 30k EU, a 60% efficient conversion. There actually is a loss-less conversion in the other direction: an electric engine with an iron electron tube converts 5 EU/t into 2 MJ/t.
The issue, as far as I can tell, is that some of the specialized engines (magmatic, combustion, biogas) are much better than their IC2/gregtech equivalent generators per bucket of fuel, so much so that even a 40-60% efficient conversion can look quite good:
The magmatic engine gives 18k MJ, compared to the 20-30k EU of the geothermal/thermal generators (about 1.1-1.7 EU/MJ). At 60% conversion efficiency you get 27k EU. So burning lava in a magmatic generator, using the energy to melt cobble into lava, then feeding that lava into a thermal generator loses 10% of the energy you would get just using the lava straight in the thermal generator - exactly what you would expect, since the magmatic engine gives back 90% of the energy it takes to make an amount lava equal to what it burned.
The combustion engine on normal fuel gives 600k MJ, on biofuel 200k MJ: the diesel generator gives 384k EU on normal fuel, 32k EU on biofuel (0.64 EU/MJ and 0.16 EU/MJ respectively!). At 60% conversion efficiency, on normal fuel you get 360k EU instead of 384k EU - a 6.25% energy loss compared to just burning the fuel in a diesel generator. Still within reason. On biofuel, you get 120k EU instead of the 32k you get burning the biofuel straight, a 275% gain in energy over just burning the biofuel straight in the diesel generator. Even using the 40% efficient conversion, this nets you a 150% energy gain over just burning the fuel straight.
The biogas engine gives 50k MJ on biomass, the semifluid generator gives 8k EU (0.16 EU/MJ again!). This gives the same 275% gain in energy over burning the fuel straight in the semifluid generator when passed through the 60% efficient conversion process again.
Looks like we have our culprit! In order to actually gain energy (or, indeed, not to lose it) from the cobble cycle feeding into a thermal generator, you have to use biomass/biofuel to power your magma crucibles (or steam, maybe; I haven't really looked at railcraft boilers yet, but I hear they're very efficient). The combustion and biogas engines are just that much better than their EU-producing counterparts (the bio generator gives the same* total EU per bucket on biomass/biofuel as the diesel/semifluid respectively, just not at the same burn rate).
If the thermal generator were as good as the magmatic engine, it would give 45k EU per bucket, not 30k. If the semifluid generator were as good as the biogas engine, it would produce 125k EU per bucket of biomass. If the diesel generator were as good as the combustion engine, it would give 500k EU per bucket of biofuel, and 1.5M EU per bucket of normal fuel! Conversely, if you brought the engines down in efficiency to match the generators, the magmatic engine would only produce 12k MJ per bucket, the combustion only 12.8k MJ on biofuel and 153.6 MJ on regular fuel, and the biogas only 3.2k MJ on biomass.
*(Well, almost the same - in direct testing, the bio generator gave 32k EU/ bucket on biofuel, while the diesel generator consistently gave me 31,992 EU per bucket, tested by hooking each up directly to an empty MFSU and feeding it a single bucket of biofuel.)