+1 on this one. I run small SMP server with one way teleporter (i don't have power plant on the other side yet). Teleporter distance is roughly 700 blocks. The thing is that after some time (usually after disconnect or server restart) even powered side of the teleporter stops workng. I have MFSU unit with 10 million EU under it so it is not matter of power. I have to manually reset teleporter link with freq trans every time...
I haven't tested it much due to the distance between the teleporters. 
I'm having this problem on my server too. It's fine for short range teleporters (we're talking line of sight- maybe sixty blocks away), but longer than that and freqtrans seem to lose their info.
For instance, let's say I have a teleporter hooked up to four MFSU blocks each full to the brim. This should be able to teleport me a fairly decent distance.
I link a freq trans to the teleporter, and then I head 100 blocks in any direction, plop down a new teleporter, and click on it to link it.
Instead, the freq-trans behaves as though it weren't linked, and I link it to the new teleporter instead of linking both.
Multiple attempts to make this work haven't yielded results- but it seems like if I move a certain distance overland the freqtrans will bug. Note: If I shortcut through the nether- and only then if I don't take too long- I can occasionally get long range teleporters linked, but it will always behave as the other examples in this thread, ie: one way.
Currently I'm building several short range (line of sight on normal distance) teleport links, going from one to another to another. It's expensive as heck, but it's the only thing that works.
