The following is based on decompiled version of Minecraft 1.9 using MCP 9.24 beta. All method and class names are the names used in the decompiled version.
It looks like the method net.minecraft.client.renderer.RenderItem.renderItemOverlayIntoGUI(FontRenderer, ItemStack, int, int, String) is not enabling blending after drawing the stack count, but I am not very familiar with how rendering works.
Caused if itemstack > 1