Google's cached images show something rather interesting. It's also something I noticed too over the numerous patch updates we've had. Although this is something I've noticed prior to Spiral Knights being released to the public. The gems look a little hard to look at nowadays
During the Beta:
http://img842.imageshack.us/img842/764/gempo.jpg
http://img37.imageshack.us/img37/6904/gemu.jpg
Post-Beta:
http://wiki.spiralknights.com/images/7/70/Token-Jelly_Gem.png
http://wiki.spiralknights.com/images/9/92/Token-Almirian_Seal.png
I'd love to see the coloring of these gems return to how they were originally! I'm surprised nobody else has noticed this!
I always thought this was an intentional art update, although I did think my graphics card was bugging out when I first saw the recolored Jelly Gem drop. :x
Also it's only been like this since the crafting cost/auto bind/boss token/ragefest/etc. update. They used the old art during release until then. :P