I can confirm that in 0.9.3c on Windows if you use the main menu (File -> Export Wallet) you end up with a file which begins like this:
[
{
  "type": "master_key_record_type",
  "data": {
    "index": -1,
    "encrypted_key": "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx",
    "checksum": "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
  }
},
{
  "type": "property_record_type",
  "data": {
    "index": 1,
    "key": "next_record_number",
    "value": 989
  }
},
Whereas if you do it using the console command wallet_export_keys and supply a file name together with a full path, you get the correct file.