The new NMM version changes the way mods are installed.
If you want to change the options for scripted installers you need to uninstall them (just as before), otherwise NMM will remember what you chose to be active in each profile and automatically restore it:
Uninstall is no longer achieved by double-clicking on a mod (that will just disable it, thus removing their link to the game's Data folder).
To uninstall a mod you need to right-click on it and select one of the 2 Uninstall options.
Now, if you reinstall it you'll get the usual scripted installer menus.
This is not an issue, but working as intended.
Currently there's an issue for a few people, that we're unable to replicate, where upon uninstalling a mod, NMM is unable to remove the xml file where the selected options are stored.
[EDIT] This could be fixed in 0.60.7 , if you were affected please provide us feedback using this version.
In the meantime we fix this, if you're affected by this issue, you can manually fix it by:
Uninstall the mod right-clicking on it and selecting "Uninstall Mod"
Go in the: Mods/ModProfiles/{randomProfileID}/Scripted folder
If there's an xml file for that mod, manually delete it then retry installing it.
If this keeps happening to you please open a report here: http://forums.nexusm...ager-open-beta/
provide info about which mod is causing the issue and what's your antivirus (security suite).