There is a similar thread here http://drupal.org/node/1852210 but for the drupal 6 version of node_export. This is also happening in drupal 7.
When exporting nodes that are linked via translation, they share a tnid value. That tnid value is equal to the nid value of one of those nodes. However, on import the node_export module nulls out the nid (b/c it is creating new nodes, and doesnt want to overwrite existing nodes). This change in nid breaks the link between the nid and tnid, causing the tnid to reference a non-existent node, or a different node all together.
I have written a patch for this. I'm not sure if it covers all scenarios, since I am not intimately familiar with the module. However, for the small imports I am doing it seems to be working great.
The patch only overwrites the tnid value when it detects that it matches the nid of a node being imported. Otherwise the tnid is left alone, so as to preserve existing functionality of importing the tnid as specified. This is a valid use case, where an existing node is having a new translation imported.