Synchronization difference - hmc vs productcockpit

We are facing a synchronization issue on hybris 6.4.

We extended Product to add a few attributes:

 <itemtype code="MyProduct" extends="Product" ....>
     <attributes>
         ...
         <attribute qualifier="someType" type="SomeProductType">
         <persistence type="property" />
     </attribute>
     <attribute qualifier="aList" type="CustomObjetcList">
             <persistence type="property" />
     </attribute>
     </attributes>
 </itemtype>
 
 <collectiontypes>
     <collectiontype code="CustomObjetcList" elementtype="CustomObjetc" type="list" />
 </collectiontypes>

The CustomObject needs to synchronizable as well, so we declare it like this:

 <itemtype code="CustomObject" ...>
     <custom-properties>
         <property name="catalogItemType">
         <value>java.lang.Boolean.TRUE</value>
     </property>
 
     <property name="catalogVersionAttributeQualifier">
         <value>"catalogVersion"</value>
     </property>
 
     <property name="uniqueKeyAttributeQualifier">
         <value>"pk"</value>
     </property>
 
     <property name="catalog.sync.default.root.type">
         <value>Boolean.TRUE</value>
     </property>
     </custom-properties>
     <attributes>
         ...
         <attribute qualifier="catalogVersion" type="CatalogVersion">
         <persistence type="property" />
     </attribute>
     </attributes>
 </itemtype>

The problem is that when we synchronize on hmc Catalog - Catalog Management Tools - Synchronization it works fine. Everything from staged catalog goes to online catalog.

But if we synchronize on productcockpit, we get an error that does not help much:

 17.09.12 10:09:15:194    INFO    Starting configuration ...
 17.09.12 10:09:15:194    INFO    Default Synch Configuration
 17.09.12 10:09:15:194    INFO    Finished configuration in 0d 00h:00m:00s:001ms.
 17.09.12 10:09:15:194    INFO    Starting synchronization ...
 17.09.12 10:09:16:366    INFO    1. pass, 9 (+9) of 0 items processed (0 %),  7,69 items/sec, 9 (+9, deadlocks:4) items dumped.
 17.09.12 10:09:16:954    INFO    2. pass, 8 (+0) of 9 items processed (88 %),  0,00 items/sec, 6 (+6, deadlocks:0) items dumped.
 17.09.12 10:09:16:979    INFO    comparing last dumps (9/8796172288030 vs 6/8796172386334) - this might take some time...
 17.09.12 10:09:16:979    INFO    done comparing last dumps - dumps are different
 17.09.12 10:09:17:027    INFO    3. pass, 5 (+6) of 6 items processed (83 %),  84,51 items/sec, 6 (+6, deadlocks:0) items dumped.
 17.09.12 10:09:17:050    INFO    comparing last dumps (6/8796172386334 vs 6/8796172484638) - this might take some time...
 17.09.12 10:09:17:054    INFO    done comparing last dumps - dumps are equal
 17.09.12 10:09:17:055    ERROR    sync ended with 6 unfinished items - see last sync media for details
 17.09.12 10:09:17:065    ERROR    Finished synchronization in 0d 00h:00m:01s:871ms. There were errors during the synchronization!

There are 10 products to synchronize.

The 6 unfinished items are the products that has a list of CustomObject. The other 4 are synchronized.

Can anyone tell us the difference between hmc and productcockpit synchronization?