I have NO idea if these will help, but some "bug" links I saved
CS6 Bug Clip Name http://forums.adobe.com/message/4654667
CS6 Issue/Bug MXF http://forums.adobe.com/thread/1074489
Same exact thing going on here. MXF clips jumple and discard random bits of footage when there are spanned clips.
We have tried everything here. The two weeks we have been working with the c300 footage in post has been a total nightmare. We scoured the internet looking for answers.
The one thing that seems to work best for ingesting MXF media is transcoding to ProRes with Final Cut Pro 7's 'Log and Transfer', after installing the FCP x Canon Plugin, then importing those clips to Premiere Pro.
Hoping for an update soon.
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. I saw one reference where someone asked about who was working off a network drive/SAN. Which I am. 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.