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part of the changes I've made to the command service use CSS opacity to deemphasize the commands when they are not being hovered. This looks nice on Chrome and FF. On IE an opacity < 100% looks raggedy, specifically in the upper right of the image. When the image goes to full opacity, it looks fine. The dojo docs claim that dojo.style using "opacity" is supposed to deal with browser differences. I tried an older trick whereby we use the style filter: alpha(opacity=50); on IE, but it actually made things worse (the 100% looked raggedy too).
I noticed that the IBM icons (gifs) did not have this problem. The problem turns out to be IE having trouble with the PNG format and transparency. Lots of warnings to "be careful with PNG on IE unless you are using the Microsoft AlphaImageLoader filter. http://support.microsoft.com/kb/294714 So I elected to save the remaining PNG files used in commands as gifs, and the problem is resolved.