Due to the fact that you're looping over all undergrounds, no matter their intended purpose, the mod currently lowers the underground distance of underground belts which are supposed to go farther. An example would be 5Dim's "5d-mk2-transport-belt-to-ground-50". I see 3 options to handle that:
1) Restrict the mod to certain set of belts (by name). White-list method.
2) Blacklist certain underground belts to being modified.
3) Just check if the resulting distance would be lower than the current one and apply modification only if it is greater.

I personally applied method 3) as it is simpler to code, for the copy I am using of your mod and it seems to work.