Ummm ... case sensitive? .... thats a little surprising!
What OS are you using? XP or Vista 32 / 64 ?
Personally I have my Mod folders all under my main ArmA directory, start them all with @
Vista Home Basic (32bit)
My mod folders are set up the same, X:\Program Files\ArmA\@""\Addons\*.pbo
Initially it was X:\Program Files\ArmA\@""\a
Short of QG and patches 1.07 thru 1.11 nothing's changed and I dont recall anything in the patches changelogs about handling addon folders so all I can assume is the mod folders "Addons" subfolder is case sensitive for some insane reason.
And seemingly its not due to incompatibility as they all worked well together from within ArmAs addons folder before the mod folders started working, and to be sure, I ran thru them individually in the editor just to be sure I hadn't been lacking any objects previously.
If it is a Vista quirk it's luckily the only one I've been nailed by to date short of overall game performance issues across the board due to what I've come to assume are the changes in how Vista handles video processing beyond the card.
But it works fine now and thats the important thing, back to the editor.