ModelConverterX uses certain default values for the material settings when you press the “Set Default Transparent” button in the material editor. On of them is the alpha test value, which had a fixed value before. But with some alpha values in the texture that could result in the transparent part not showing up properly. This would mainly happen with parts that are very transparent (alpha value between 0 and 128).
Today I have changed how ModelConverterX sets this setting and it now also looks at the texture you are using. So if you have a low alpha value, the setting will be adjusted to that. This will hopefully result in more objects with transparent textures working out of the box when converting with ModelConverterX.