What is the difference between the two empirical p-values, EMP1 and EMP2, generated by permutation, using Plink?

The only description they give is the following: "two sets of empirical significance values can then be calculated -- pointwise estimates of an individual SNPs significance, but also a value that controls for that fact that thousands of other''

As far as I understand is that EMP1 is after a 1000 permutations and EMP2 is after adjusting for multiple testing. OR is EMP1 only after a proportion of permutations have been performed and EMP2 after the full 1000 permutations?

For a result of mine the EMP1 result is significant (p<0.05). However, the EMP2 is not - What does that mean?

Please help.