Right, just pick your input and and an output file name and go.
It will just copy the MKV as is, no transcoding. But the header fields will be created new and we've found that the utility populates fields that the player needs.
mkvinfo is part of the same package.
mkvmerge also has a header editor. It would be interesting to discover whether we can fixup these files just by editing certain fields in the header rather than recreating the whole file.