I'm not sure why it's doing that, but I think what you're doing is kind of non-standard. You're creating a GIF out of an Animation, but an Animation is sort of a special UI "object" (it's ultimately a Manipulate). I could be wrong, but I think maybe you aren't exporting your raw frames but instead this special UI "object" according to some internal rules of Export.

When I create GIFs, I just create the frames and export them as GIF. Something like this:

a = Table[ListPlot[{{1/2, x}}, PlotRange -> {{0, 1}, {0, 3/2}}, PlotStyle -> PointSize[0.03]], {x, 0, 1, .1}];
Export["/Users/eric/MathematicaCommunity/a.gif", a]