The problem in your case might be that you have the special parts anywhere on your hard disc. If you use the browse windows and add that part, all looks fine. But if you close the model file and reopen it you do not see the special part anymore. Correct.
If this is the case, please just copy the special part to the same location as your model file (no subfolder!).
If you now open your model file all will be visible again.
Reason for this behaviour:
MLCad and most other application only uses the standard ldraw library folder to search for a referenced file.
But always the current folder of the model is also checked.
In the model file there will be only the filename stored. If you like (not recommended) you can specify a path on your hard disc.
I hope this answer is not too confusing
If this is the case, please just copy the special part to the same location as your model file (no subfolder!).
If you now open your model file all will be visible again.
Reason for this behaviour:
MLCad and most other application only uses the standard ldraw library folder to search for a referenced file.
But always the current folder of the model is also checked.
In the model file there will be only the filename stored. If you like (not recommended) you can specify a path on your hard disc.
I hope this answer is not too confusing