There seems to be variations of the icon image, and I'm sure they mean something. The standard appears to be a blue box with an X in italics. And, some have a little 'circle' in the bottom left of the standard icon image. I have seen a blue circle with an plus in it, a red circle with a plus in it.
What do these mean, and what are the other variations and their meanings?
You have a Visual Studio snapin for ETL development that is causing the icons to get an overlay image. I know of two products that do that. I am not familiar with the glyphs you are referencing but they generally indicate an item configured using expressions or
Below is BIXpress
BIDSHelper (free) calls them SSIS Variable Window Extensions
Finally, SQL Denali aka SQL Server v.Next will have "Icon marker (“Adorner”) to indicate Connection Managers and Variables with expressions" (Look really hard and you will see a little fx symbol in the corner of InputFile connection manager)