66 blocks are wired in this order (4 pair cable) from the top:
w/blue (bl)
blue/w
w/orange (or)
orange/w
w/green (gr)
green/w
w/brown (br)
brown/w
If you need to move the pair order around you should do that with crossconnect wire. Mforrence's post may have hit the nail on the head. You likely have a cross up in the second pair. On the 66 block the second pair is ORANGE, on a 568B jack the second pair is GREEN. 568A is more in keeping with telephone work. So you likely have three choices (my preferred order):
1. Reterm the jacks to 568A.
2. Fix the pair 2/3 reversal with crossconnect wire at the 66 block(s).
3. Use nonstandard order on the 66 block (bl,gr,or,br).
What kind of phones are these?