Seems to me that it's possibly a normal operation.

The song contains Start/Stop markers and the new midi file is showing it's markers too?
Are you doing just a single file or multiples?

Do you get different/better results if you:
"You can also drag-and-drop any Instrument Part to a location in the File Browser to export a Musicloop or MIDI file to that location. As you hover over the Browser, you can press [Alt] to choose between Musicloop and MIDI file formats. If you drag-and-drop multiple parts at once, they are written to one MIDI file with multiple Parts". (Page 327 in S1 4.0 PDF Manual).

What is the end result you're trying to achieve?

Thanks for the reply. They are complete midi files, bass track, kick track, Piano track etc etc. The drag and drop approach doesn't include the tempo unfortunately, that is why I have to "save as midi file" Yeah sure when opening the saved midi in Cakewalk, markers are fine, but when reopening in Studio One you get duplicates.

It`s not a show stopper or anything, but you'd think that Studio One could at least check for markers before adding duplicates. "Upon opening If start and end markers exists then don`t add new ones"

If you need to re-edit any midi files after the first save, subsequent saves will just keeps on adding new start and end markers and it starts to look messy. You have to remember to delete the duplicates first before saving again.

Just an update I had a reply from support and they are now aware of the issue and will hopefully be addressed in a future update.

Maybe a needless post on my part...

So "Support" says it's a bug... OK then.
Thanks for letting us (or those who see this post) know.

Nothing is ever needless, it could of been something simple I was overlooking, just so happens it`s some kind of bug, like I said it`s not a show stopper, but better to be fixed than not

Shame this issue hasn't been fixed in 4.5.3