We installed an external ATC system, patched our SAP landscape up to Netweaver 750 PL 16 to check our own developments. But checking code in modification was possible in some, but not all development systems.
Checking for notes or internet did not help. Remote version comparison of SATC (sub)packages between working and non-working systems, did not deliver any hint. ATC setup was the same.
In the end, after some debugging, I found out that we had a corrupt namespace in some development systems. The namespace was flagged as SAP namespace with role P (producer). This caused the ATC check to fail.
You can see the namespaces in SM30 using V_TRNSPACE.
PS: In our case it was namespace /0SJ1P/.