We frequently see a similar problem, and we constantly are applying the latest ME patches. We are on 6.1.4 Patch 25 today, and will apply Patch 28 as soon as it becomes available. (We are still in development - no production yet -- so we have the luxury of being able to do this.)
Anyway, this issue comes and goes for us. Frequently, if you look in the NW developer trace, you will see an error. It is logged when you do Configure Links in MII. The error has varied a bit , but is (as I recall) usually a JAXB (serialization) error.
In our experience, if you go into Service Extension Maintenance, select the same service method, and do View Input/Output, you will get an Internal Error (on the UI). And if you then go look at the NW logs, you can get the same error that is triggered from MII. For those of us who are infrequent MII users, this is an easier way to reproduce the problem.
I recently experienced this issue because I had created a custom service that used the DateTimeInterface as the type for one of the parameters. Although this is done in other ME API interfaces, it caused a JAXB error which clearly stated that JAXB does not support interfaces! I changed the parameter type to the (deprecated) java Date type, and it is working fine now. I suspect that there is a way to annotate a DateTimeInterface parameter to avoid the problem, since SAP is doing it. Suggestions are welcome!
If you get this error on a core ME API method (and you are already on a recent patch level), I would suggest that you open a ticket with SAP for correction.
For SAP: Please add a simple test case that applies to EVERY PAPI change that touches a public interface: View the input/output structures in Service Extension Maintenance, and make sure that this doesn't generate an error!
--Barry