Yes. I had this same problem. Do you have a userSetup.mel script? MJPolyTools might have over written the one that comes with the Bonus Tools.
What I did was I made a new script I called bonusSetup5 out of the userSetup.mel that came with the BonusTools5. Then my userSetup.mel just calls bonusSetup5; & MJPolyTools; to initialize them both.
If you are using Maya 5, you can use my scripts. Otherwise you'll have to adapt them, but the process will be the same.
Let me know if this is unclear.