We found the following issue in Build 39.1111 and also in 41.1151:

If a user has more than one personal/shared address books the mobility connector syncs all of them to its cache and than to the device even if you select only a few of them in the user´s setting at the GroupWise connector.

This is a problem, if the user has e.g. a shared address book with thousands of contacts like we have.

Not sure, what the real reason is, but repeating this steps resolves it somewhen

- delete user from mobility connector
- change the address books for the user in gw connector and save
- delete cache of gw & mobility connector
- restart gw & mobility connector
- add user to mobility connector
- check the folder list for the address books