Turns out there's an updated version of VecMulti that requires a slightly different format for the menu file. The menu created with MenuMaker 0.3 would show extra characters on those VecMulti cartridges, resulting in the names shifting.
Starting with Page 2 the names would no longer line up with the numbers 1-4 (game 1 on page 2 is AllGoodThings).
With the help of @NeonPeon I've been able to reverse engineer the new format, and have updated MenuMaker to support both versions.
By default the menu will be created for the Original VecMulti. If the resulting menu is shifted, then select 2019+ VecMulti to create the menu with the new format. The selection will be remembered.
Also fixed a one-off bug I discovered in version 0.3 that caused the last game in the Games directory to not show up in the menu.
Program with Source