Hey Tom. Well I manage my load order with OBMM and install my mods with that. Then I use WB to resolve conflict issues and to merge what I can. So far it works well for me like that.
Some of my mods are green - but a few of these aren't. Yes I marked them mergeable and it said that it was mergeable when I right clicked merge file. The mod did not show up anywhere in the Rebuild Patch area (you know, where you can click and include stuff), but I thought that was ok especially since the mods I loaded aren't graphics. Like, the one I loaded yesterday was "Less Annoying Dawnfang", which just puts a ring into your inventory so that Dawnfang will not drop off your hotkey. Also I'm using Improved Hotkeys - that one also says that I can merge it, and when I do everything looks great, except it doesn't turn green, so I can't turn it off in OBMM.
I can just accept it as "that's the way it works and I don't know why it turns some green and not others" but I'm curious and want to know.
One comment I would make is to uncheck mods in Wrye Bash rather than OBMM - not sure whether this helps, but it doesn't seem logical to disable mods in OBMM (even if you are using it to install and adjust the load order). If you mark the mod as mergeable and it doesn't turn green, implies there may be an issue - surprised that WB doesn't tell you.
Which version of WB are using?