The flower texture is not verticaly centered:
There are 5 pixels on top, and 7 pixels on bottom, the pattern must be move 1 pixel on the bottom.

On banners, the flower pattern is centered.

Commands to reproduce the bug:

• Generate a shield (with vertical alignment problem):

  /give @p minecraft:shield 1 0 {BlockEntityTag:{Base:0,Patterns:[{Color:4,Pattern:"ms"},{Color:15,Pattern:"flo"}]}}

• Generate a banner with the same pattern (without the problem):

  /give @p minecraft:banner 1 0 {BlockEntityTag:{Patterns:[{Color:4,Pattern:"ms"},{Color:15,Pattern:"flo"}]}}