I am using the ManyManyDataobjectManager- going well except one small bug. The TreeDropdownField doesn't work in the popup, if I switch to ManyManyComplexTableField then it works. I had a look and they have just added some new js requirements into those form fields /sapphire/forms/TreeDropdownField.php and /sapphire/forms/TreeSelectorField.php
They have added:
to both so I imagine it's now conflicting with something of yours.