Dear mugz,
Thank you for your post.
Could you please let us know what version of Video Splitter you use?
Could you please upload for us the MKV file you have tried to edit to any file host service, e.g. dropbox.com or filedropper.com?
Also please send us (you can use support(at)solveigmm(dot)com) the project file. To get it select fragments for saving then go to File -> Save project as.
Thank you in advance.