Thanks for the reply Shane,
Yes, it’s mp4 format and i’ve realized that FCP doesn’t like it much, was hoping for an easier way out but oh well c’est la vie.
I have about few hundred clips to edit and instead of importing and then exporting them to/from FCP as mov files one by one it is faster if i import them (mp4), edit and do motion changes then export them in mp4, import once again and export in mov and finally import the video once again, cut it up into the previous clips and do SmoothCam and then export in mp4 as that’s what the upload application prefers.