The computation of NFRC U-factors and SHGC values involves an iterative process to achieve a stable temperature profile within the glazing. The net energy flow is computed once temperature differences betweeen 2 iterations are below a threshold value. This value has been 0.0001 (K) up to now.
Starting in CODE version 4.20 you can individually set the threshold for each integral quantity. In particular, you can set smaller values to avoid (very small) differences between CODE and WINDOW results for U-factors.