Another update.... It seems the "problem" wasn't with the EFLAGS, but with the OBJECT_FLAGS attribute in the SDE.TABLE_REGISTRY table. If I take my old table (the one that originally did not work), do not change anything, but only copy this attribute from the table that was created using ArcCatalog and overwriting with it the OBJECT_FLAGS attribute of my old table, the geometries display in ArcMap regardless of their "validity" (also no warnings or errors in SDE log files). Unfortunately I have no idea what this OBJECT_FLAGS is besides it is another binary attribute. I simply copied a value of 147463 over my old value of 133. This is not a perfect solution, but it works for now. Will try to reach ESRI's tech support on this. Anybody perhaps knows the structure of this attribute?