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That is because fonts are usually non-interchangeable unless you splice them in an editor; if you have 1 mod that changes 1 icon, and another mod that changes another, only one of them will actually get loaded. Weapon icons are, for the weapon selection are, strangely enough, saved into a true type font file, or .ttf
You'll likely run into this problem the most trying to put HL2 mods that contain custom icons into Synergy because synergy uses its own font file for its own weapon lineup, and vice versa.
As long as it remains a graphical issue, your best fix is to just remove the custom font file from the mod you're using, or use one or the other. Or learn to ignore it.