The title pretty much sums it up. I had purple saves previous to adding the Imperfection mod by DeathclawAlpha. Now my saves are orange. Once I installed the mod, I used the Master Update option from FO3Edit. Then I used BOSS to sort my load order (I'd love to post it here but I can't figure out how) and rebuilt my Bashed Patch. Once this was done, I used the main FO3Edit option to create a Merged Patch.esp, which I then placed at the very end of my load order. When I click on the save, there's a box to the right which shows all the mods and load order in which the saved game is dependent on. A bunch of these mods are now marked with orange boxes. None of my mods in my mods list have orange boxes next to them. Any ideas?

The Merged Patch in FO3Edit is not something you can just run and go, there is a lot of manual tweaking to get it right. You also don't want to mix the functions of the Merged and Bashed Patches, use one or the other. Better is to use Wrye Bash/Flash for the Bashed Patch. The only time I can see to mix the two patches is if you use Wrye only for the Tweaks.

I bet if you rebuild your Bashed Patch without including the Merged Patch, paying attention to each section and selecting what should be in there, it will sort this out.

Also, in Wrye Bash is an Export function that will copy your load order, (IIRC it even includes the Spoiler Tags), to the clipboard, so you can paste it here.

I was always curious whether using the bashed patch and merged patch at the same time was a good idea. I'm going to give it a shot and hope for the best. I'll be back with the results.

Edit: Just removed the merged patch, rebuilt the bashed patch, and I have the same problem. Also, the option on WB you were speaking of is the List Mods option. That was the one I initially tried pasting. This forum has a "Spoiler" option. I thought that would allow me to do the same but I had no idea how to use it. I've had this problem in the past and couldn't figure it out then either.

Just paste the text in the post, then select the text, use the BBC Code box just to the left of the Font button and choose Spoiler

As for the Orange mods, it is because you have a delinquent Master, in other words, the Master file is loading after the mod that is dependent on it. One thing that can happen with a new install of Bash, do you have the option checked to Lock Timers? If you do, then the mods will have a messed up load order, even after using BOSS.