just to underline your point: we have had the same issues since CS6 and it persists until today (CC 7.01).
What makes things even stranger is that I had a 55 min+ clip (from a Canon C300), spanned into 11 MXF segments.
When I imported it via the Media Browser from a portable hard drive it came in as a single clip maintaining the correct order of the segments. I then copied the hard drive's contents to our SAN (maintaining the file structure, of course).
Then I imported the clip again, it came as one clip like before - but the order of the segments within the clip was completely random, every 5:15 min there was a visible "cut" within the clip.
So maybe PPro uses some hidden metadata of the files to determine their order and those metadata get lost on their way to the SAN. I can only speculate.
I tried creating new projects, using a windows machine instead of a Mac, but to no avail.
Our temporary (yet annoying) solution is to "destroy" the files structure and then import and concatenate the segments manually.
Are you on a SAN?
POSSIBE SOLUTION - I too have had the problem with PP re-ordering C300 spanned clips. I have read many posts about this - some claiming its a Canon firmware issues - others waiting for Adobe to fix. after seeing your question about being on a SAN - which I am - it made me think. My colleague however who was editing to same project on his system (and not working off a network drive) was not having the spanned clips re-ordining issue. Same media - same project file. So I transferred all my media to my local hard drive, my colleague sent me his project file. I openned in CC and relinked the media to my local drive. All the C300 spanned clips opened in correct order, all behaving normally. I strongly suggest people who are working off network drives try bringing their media onto their internal hard drive.