I think we're talking about different things. I'm talking about the plugin list in the masters window when you have the Bashed Patch highlighted. All esm's have always been blue there for me - and all esp's green. I doubt it is caused by the Bashed Patch not using everything in the esm as all esm's presumably would be green then. But nevermind, I had to let Fearsome Magicka and thus Screen Effects go because of CTDs so I'm in no position to check it out further anyway.
A little clarification because this was bugging me, after I examined my entire mod list.
For most mods, in the masters window, Oblivion.esm is almost always the only blue CHECKBOX. Bash documentation doesn't explain the difference between blue and green checkboxes, it simply states that both colors mean the health of the mod's master files are "good". Blue TEXT indicates the file in the master window is an ESM.
For my entire load order, excluding the Bashed Patch, Oblivion.esm is the only blue checkbox. Any other ESM dependency or rare ESP dependency has a green checkbox. The major exceptions to this are Item Interchange files, which usually are all orange and red dependencies (and are supposed to be inactive).
The patch has different behavior in this window, with about half of my ESMs being blue. The first one that is green is the first one that occurs AFTER the first file in load order that
isn't listed. I believe color has to do exclusively with order here, because just as with save games, as you proceed down the list, the color will never "improve". i.e., you won't get a blue checkbox after a green one, or a green after an orange. The only exception to that rule is that file health returns to orange after red (which indicates an entirely missing file).
Can anyone more knowledgeable than me shed any extra light on this? What is the difference specifically between a blue and a green checkbox in the File Masters window?