The best solution is — once you get the panels just the way you want them — save it as a custom workspace (Window > Workspace > New Workspace)
Then, whenever it gets messed up (and it will, inevitably), you can choose Window > Workspace > Reset to get it back to its original form.
More here:

Clean Up in Aisle CS4: Resetting Workspaces

Actually, I didn’t think of this before, but this article might help:

Easier import of complex Excel spreadsheets

I wonder if there is something odd about that particular book file? What happens if you place the files in a brand new Book file?