I'm running a pretty crazy kitchen sink modpack of my own design on a computer that really shouldn't be able to handle it. Yet I still get, even at the worst of times, 19-22 FPS. I recently updated Flux networks to both of the versions listed in the title and in the same areas I was getting 5-6 FPS. I tried downgrading back to 3.05 and my FPS jumped back up to 19+.

Can you provide any more details on what blocks/combinations are lagging? And is this single player, or does it also happen on servers?

Well I have a controller, eight flux points, and two flux plugs. In my main base, where the lagging is the worst, there is the controller, five of the points, and one of the plugs. The mods the plugs and points connect to are mekanism, nuclearcraft, refined storage, actually additions, and xnet. Breaking the controller didn't seem to help with frames. I also individually broke each plug and point one at a time and reconnected. The frames were not assisted by this either. I never tried breaking everything as that could cause quite a bit of chaos to my manufactory. The compact machine where my ore quintuplication and nuclearcraft reactor reside also contain two points and one plug, but the frames were acceptable in there.

Also this is single player.

If I had to make an educated guess, the system that registers energy transfers from within each point, plug, and controller might be the aspect that weighs everything down. That is the aspect that is most notably new with versions 3.06 & 3.07.