SDI and window management of non-TopComponents

Our SDI application uses a mixture of TopComponents and other non-NetBeans-managed windows.
We have a major problem with the upgrade to NetBeans 6.0 and its elimination of SDI mode: now, whenever a TopComponent is activated, all other TopComponents pop to the top, thus obscuring our other windows.

We do not have the option to convert all of our windows into TopComponents.

How can we disable this new NetBeans "feature" that assumes all TopComponents need to be on top of all other windows?

I hope it doesn't require changes to any NetBeans source code, but if it does, I would appreciate any advice about where to look and what to change.  We don't want to go back to a pre-6.0 base, but cannot use the system as it is.

Thanks in advance,
Roxie