This answer build's on JoeK's; I think he points out the problem but what went wrong may not be obvious.
Rims can have offset holes for different purposes, but the rims in question here have them for potentially all the purposes depending on the build choices. An average, holes-running-down-the-center (or nearly so) rim will frequently have some small amount of offset side to side to match the side of the hub the spokes are intended to run to. Usually the amount of offset in rims like this is negligible for spoke length calculation purposes. But, if you are building your Rabbit Holes (or other 64-hole Surly rims) such that the drive side offset holes are going to the drive side flange and vice versa for the non-drive-side, you are building a wheel where the effect on spoke length won't be negligible.
The confusion point can be that "normal" offset/asymmetric rims that still only have one set of spoke holes are doing something completely different. On a rim like that, all the holes are offset from the rim centerline in the same direction, whereas on your rim they are offset in alternating directions.
There are three ways you can build up 64-hole choose-your-own-adventure type rims like yours, and each could make sense depending on the application. Using a calculator such as Freespoke that accepts a different offset value for each side of the wheel, the options would be:
- The DS flange spokes go to the DS rim holes and the NDS flange spokes go to the NDS rim holes. This would tend to be the choice that goes along with the really wide fatbike rear end spacings. You would enter both offset numbers as positive values.
- The DS flange spokes go to the NDS rim holes and the NDS flange spokes go to the DS rim holes. This a way of maximizing the bracing angle and I see some people have built their Rabbit Holes this way. For this you would use a negative offset value on both sides.
- The DS flange spokes go to the NDS rim holes and the NDS flange spokes go to the other NDS rim holes. This would be done for the same reason as using an asymmetric rim; to get a better bracing angle on the drive side spokes and more even spoke tension, usually on a non-fatbike-specific rear end. (Where my working knowledge ends is where the cutoff is in rear end spacing for the different modes to typically make sense, but the good spoke calculators nowadays all will show you with the bracing angles and the L-R tension balance so you can see for yourself which option does what). To do this you would enter the DS offset as a negative value and the NDS as a positive. (For a front it would be the opposite, non-brake-side positive and brake side negative.)
If your DS spokes are coming out too long, likely what's happening is that you've done the calculation for that side using a negative offset value where you needed it to be positive. A likely way you could have gotten to that problem is you're building the wheel using the first of the above options and you used a spoke calculator that's not set up to handle alternating offset rims. If the calculator you used has just one single "offset" value to fill in, then what it's doing is assuming you're building a normal offset road or mountain wheel with an asymmetric rim (a WTB Asym for example) and it invisibly calculated the DS spokes as though their holes were offset to the NDS, not the DS.
You can use calculators like that to build alternating offset wheels, but you do it by running the calculation twice, once with a positive offset value entered and once negative. I believe the main way of adapting the classic spoke length formula to the situation would be similarly running the calculation twice, and spoofing the "hub width" variable differently each time (I could be wrong about this).