I think I solved the mystery. The difference in displacement appears to be because a SEP slug from a previous year, probably 1943, was used in place of the 1945 slug. here's an image that I think demonstrates that:

The center cancel is a genuine SEP 2, 1945 cancel. The one to the right is the one that had me baffled. Looking back through all the Victory, VT, covers I have I noticed that the 1943 cancels lined up to the right of where the genuine 1945 cancel lines up relative to the "T O" in "V I C T O R Y." In the bottom panel of the image, I highlighted the SEP and "T O" of a SEP 3, 1943 cancel in my collection, and copied it over the cancel on the right, lining up the "T O" of the two images. It shows almost exactly the same lateral or horizontal placement for the SEP.
My theory is that sometime after September 1945 the postmaster backdated some covers (I have five like this) with a SEP 2, 1943 with a slug from a previous years set (likely 1943) thus creating the different placement. Had the slug from the 1945 set for SEP been used, it would have been harder, or maybe impossible, to know that these are backdated covers.
Basil