I am actually running into a very similar issue. I have some TDMS files that can be opened, some others (usually longer files) cannot be opened. I get the same -6211 error when I try to call DDC_OpenFileEx. I haven't been able to nail down any specific feature of the files that causes this. Both files have some timestep channels, some waveforms and about the same metadata.
I have also determined that this issue is specific to 64-bit Matlab. I used a 32-bit version of Matlab and the error did NOT occur. I also had someone compile a simple C program to open the files using the DLL and it opened all the files fine, in 32 and 64-bit form.
I have determined that for my files a defrag operation resolves the issue. This can be done in Labview or Diadem. I even made a 32-bit matlab fuction to read all the channel and metadata and copy to a new file; that also resolves the issue.
I have an open ticket with NI on this, I'll let you know if I ever get anywhere.