Question's:

When I go into Wrye Bash it tells me "An invalid Plugin load order has been corrected".

OK - fine : Wyre Bash should know best

When I start the SkyrimLauncher (Data Files) to check if all mods are checked and ready to go I notice 2 esp's that are not checked:

http://skyrim.nexusmods.com/mods/9960
http://skyrim.nexusmods.com/mods/2275

OK, I check them and close the SkyrimLauncher and open Wrye Bash, it tells me that there is "an invalid Plugin Load order has been corrected"

OK, go back to SkyrimLauncher (Data Fles) and both esp's are unchecked again.

1) What is going on here?
2) Leaving them unchecked in the SkyrimLauncher (Data Files) means that they are in the game?
3) What can I do to rectify/understand the issue?

Observations:
- NMM has both esp's checked even if they are unchecked with SkyrimLauncher (??)
- BOSS is always been used, so no load order issues
- I use SKSE_Loader (desktop shortcut) to start my game every time

I've been getting the "An invalid plugin load order has been corrected" pretty much any time I do anything in Wrye Bash, move stuff around, switch tabs, rebuild my patch, simply tabbing out of the program and returning.

Just check what you want in Wrye Bash and start playing, should be fine.

So even if Wrye Bash inactivates the esp's "only" in the SkyrimLauncher data files then they will still work - yes?

Check 'em in Wrye Bash and pay no heed to the Launcher. I stay as far away from that thing as I possibly can.

Ok, thanks for the heads up.

I still would like to know why this happens - maybe I should of posted this in the Wrye Bash thread or maybe someone has a good explanation?

Just to let everyone know !!!

It is incorrect to pay no heed to the Launcher, if the esp's are unchecked then they do not work properly. If Wrye Bash uncheck's them only in the Launcher and not in NMM and Wyre Bash then they are still not activated.

I tested on the Improved Skill books and noticed it immediately that it was not active however it was in Wrye and NMM active........

I have no idea why how this happens and start wondering about how this can be resolved?

Well, if you activate them in WB, then check the launcher and see they're not active, and then launch the game, of course they aren't present in your game, as the Launcher deactivated them. But if you activate them in WB, then start the game (via the link in WB is my recommendation), everything should be fine. Like I said, stay away from the launcher, it also likes to reset your ini files without warning.