A ton of the mods in FTB are very poorly coded *(eg. to check if solar-panels can see sun, they use the dumbest algorithm possible:  a `for` loop that checks every y-value above it for blocks **every freakin' server tick**)*.

To test if this is your issue, try going far away from your main-base to someplace you've never been.  If the "lag" stops, then the problem is most likely a CPU-hungry mod.

There's not much you can do about CPU-hungry mods except turn them off, or *(in single-player only)* just promise yourself not to use blocks from the laggy-mods.  Because it's a CPU-issue, reducing the graphics won't help.  You could try increasing the process priority, but that likely won't help much, and could cause stability problems.

Unfortunately, there's no ultimate-list of laggy mods that I know of, and the list changes with every version anyways.  Check the FTB forums, and see which mods most server-administrators are currently disabling, and why.