Problem applying Paragraph styles in CS4 InDesign

I boughtCS4 InDesign for Windows perhaps six months ago, and it worked fine with Windows XP. I have recently installed Windows 7 and find that the paragraph styles won't always work. Of ten when I try to use the shortcut for paragraph style the paragraph in question turns pink with small squares in it. If I undo the application of paragraph styles it goes back to text. I am using Times New Roman as the major font. However, I have tried other fonts and they won't work in paragraph style either.
I tried changing several pages of the manuscript to Times New Roman Special G1, but it won't do the commas, quotes, etc. (special characters).
Has anyone else had this problem? What can I do to fix this mess?
Thanks for any help.
Earl Davis

Well, here's the situation now. But before describing it, let me thank Peter
Spier and Bob Levine who have endeavored to help me. Now, here's where we
are:
I copied a document over from Pagemaker into InDesign using Times New Roman
font. (I did the same for two other book manuscripts this past summer,
shortly after purchasing InDesign and had no problem). Suddenly a couple
weeks ago I found that the shortcut I set for the paragraph styles did not
format the paragraphs, etc., but rather turned the paragraph in which I
placed the cursor into a series of pink squares highlighted in pink. I have
tried the suggestions you fellows have given, such as copying the fonts
presently in the Windows Font Directory into the Adobe/InDesign/Fonts
directory, and then right-clicking on them and installing them. By the way,
the InDesign font directory only had the Times New Roman and Times New Roman
Special 1 and Renaissance font in it, until I copied all my fonts there and
installed them. Another oddity, I make the first letter of the first
paragraph of each chapter a decorative Renaissance font, spanning two lines.
I now find that when I do that, I may get a black square, which may turn
into the correct font after I adjust the size to two lines.
   But on the general problem, I have tried changing the font in the
paragraph styles to Amerigo BT, and I sometimes get the shortcut to work,
and sometimes it still turns it into Times New Roman Special or black
squares. Also, I have opened a new file and put another copy of the text in
it, setting up the paragraph styles, etc. and still have the same problem.
   So I'm at a loss what to do.  I do think it's possible I am doing
something wrong with fonts or setting up the paragraph styles, but I don't
see any errors there. All my computer fonts show up in the fonts panel of
the document.  Any more ideas?

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