Had same issues with my Vixia HF100. A maddening detail Canon neglects to tell you is that longer clips are split. Not in the camera’s viewfinder playback – it’ll obligingly and secretly stitch the split clips together and play them seamlessly…the only hint is your noted discrepancy between number of MTS files.
You need to join the files back together, something I found on Voltaic’s site which now mysteriously only has the “why,” but no longer has the instructions on how… fortunately I saved them, though you’re SOL if you’re not on a mac.
File joining on the Mac
The Mac solution requires running a command under the Terminal. Many users will not have had to do this before, but don’t worry – its easy. Just follow these steps.
Open a Terminal window. The Terminal application can be found in your Applications folder under Utilities
Go to the directory where your spanned clips are located. You will need to use the Unix change directory command ‘cd’
cd Movies/MyAVCHDclips
{i.e., ‘cd’ followed by path to your MTS files, using / between folders/file}
Enter the following command and press Enter:
cat file001.MTS file002.MTS > newfile.MTS
{where file001.MTS and file002.MTS are your files to be joined.}
This will take a while! Leave it for at least an hour before checking on your results.
{Note- for me, it only took a few minutes}
Hope this helps.