Native framerate or not ?

I'm shooting using .mts format and the H.264 codec in HD1080 at 50i

I'v converted a test clip from.mts H.264 into .mov apple jpeg photo and it looks good.

When I upload to pond5 says the framerate is 50 frames per second.

I seen everyone uses standard 29.97 or 25 fps.

Should I then deinterlace to 25 fps ?

Jpeg photo or photojpeg is progressive, mjpegb would be interlaced. If you start with interlaced footage, you should probably keep it interlaced. Hence, 50i. 25 FPS would be considered progressive. Of course if the software de-interlaces it, it would show at 25 here on P5. So your clip is interlaced and most likely it would have been rendered as a mjpegb, not photojpeg. Double check your settings on the codec and make sure you are using mjpegb (in some rare cases mjpega) for the final output. That would be my best guess. :)