We have used the calculation for theoretical void time that John Dolan and others refer to for some time as the default value in methods (actual t0 is determined during blank injections).

However, we are not sure how the calculation came about and why one of our methods has an actual t0 much more than the theoretical (same on multiple instruments. Flow rates have been verified as correct).

Anyone able to help?

John's "0.6 x the column volume" is a rule of thumb, no more. My rule of thumb is "2/3 x the column volume".
The column void time comprises the volume between the particles, and the proe volume inside the particles. The volume between the particles is always about 40% of the column volume (give or take 2% unless you are using compression techniques). The pore volume of a packing can vary significantly, from 0.25 mL/g to 1.2 mL/g. Many underivatized silica packings have values between 0.5 mL/g and 1 mL/g. This translates to a fractional porosity of between about 0.5 and 0.66. Therefore about 50% up to 66% of the remaining 60% are pores in a silica column. This means that for a silica column, the dead volume is between 70% to 80% of the column volume. If you are dealing with C18s. part of the pores is occupied by the C18, and you get numbers which are a bit smaller.

Pfff that was way to long...

As usual, Uwe is correct. The pore volumes can vary greatly between packing materials. Take 2 C18 columns with 5 micron materials that have listed pore diameters of 100A. The pore volume of one could be 0.6 mL/g (not a lot of holes) and another could be 1.1 (a lot of holes). Assume that for a 250 mm column with a 4.6 mm ID you can use a couple grams or more of packing and you can see how the V0's would be very different.