I have not been able to replicate the conditions to repeat this issue, but I was cloning an active object and editing it (copy and pasting different graphics in from Photoshop). The active object had two frames of looping animation. After the third clone operation (so I now had four versions on the frame), when I ran the frame only the last active object appeared. Looking in the debug window the other three were not there to add (only this fourth one).
They all had the same properties, to be created at start for example. Changing any of the properties had no effect, the other three active objects would not appear in the game when I ran it.
I have saved my MFA and closed/reopened and this issue in no longer occurring, all four active objects are now appearing when I run. Sorry it is not a lot to go on, thought better to report it.