Well perhaps what is not in the right place is not the mods but the installers.dat file.
Does its location match what you have on your ini?
I posted about some wrangling of these ini entries http://www.gamesas.com/topic/1084204-bain-mod-installation-projects/page__view__findpost__p__15798007.
[edit] as an example of something I wish bash did natively is to have the installers.dat and bashmoddata.dat files local to the game install (in the MOPY folder). This way I can leave all the bloated amount of mod archives on yet another hard drive and don't have to burden my already bloated steam folder with gigs of mods).
My ini for that:
[General]
;--sOblivionMods is the Alternate root directory for installers, etc.
; It is strongly recommended that you do NOT put it anywhere under the
; game install directory itself, because Oblivion.exe will search through
; every directory under the install directory.
; This "directory thrashing" can then cause performance problems during gameplay.
; sOblivionMods is defined specifically to circumvent this bug by storing files elsewhere.
sOblivionMods=H:\BAIN Archives\Skyrim Mods
;--sInstallersData is the directory containing data about which installers
; are installed by Wrye Bash. This is where 'Installers.dat' and 'Converters.dat'
; are stored. Only change this for advanced configuration, such as when using
; mTES4 Manager or MOM to manage multiple Oblivion installs. In those cases,
; it is recommended to set this to a subdirectory of either "My Games/Oblivion"
; or "Oblivion/Mopy", so mTES4 Manager/MOM will move these files when changing
; clones/images.
sInstallersData=http://forums.bethsoft.com/topic/1372611-help-with-bain/G:/Steam/SteamApps/common/Skyrim/Mopy/BAIN
;--sBashModData is the directory containing data about your mods, ini edits, etc.
; Only change this for advanced configuration, such as when using mTES4 Manager
; or MOM to manage multiple Oblivion installs. In those cases, it is recommended
; to set this to a subdirectory of either "My Games/Oblivion" or "Oblivion/Mopy",
; so mTES4 Manager/MOM will move these files when changing clones/images.
sBashModData=http://forums.bethsoft.com/topic/1372611-help-with-bain/G:/Steam/SteamApps/common/Skyrim/Mopy/BAIN
But with the ini you can set it to however you like. I like it so that the BAIN archive is just mod archives and the game folder is where to find the info on what is read from that folder. Makes more sense to my brain.