After checking and executing "Clean Motion Objects" in Part Cleanup, I tried to run Part Cleanup again, but it was unchecked. It doesn't seem to be memorized in the dialog.
Reproduced Steps:
1. Open a part
2. File > Utilities... > Part Cleanup... > Clean Motion Objects=ON > OK
3. Again perform Step 2 above
This behavior is due to NX problem and is fixed in NX 2406.
Workaround: check it on each time.
Notes**Please refer to PL8777281 for Japanese article.