I thought the problem had gone away last night. I made a Magic Map and found a large hollow hill, which I slapped a Filler on to slice the top off (completely draining two RECs in the process). I was clearing out the revealed loot and killing off the occasional ghost, when suddenly the problem came back. The game would pause for about a minute, and then I'd get about three seconds of normal activity followed by another pause. I stumbled over to linkbook back home and logged out since it was late anyway.
If you haven't done the chunkloader thing I would HIGHLY suggest it. I had the same problem. To find out if it is your problem go into where your FTB launcher saves everything and pull up your latest log and if it has a line near the end about a world leaking it IS your problem.