carolf123, try this:
Right-click on the callout box icon as it appears in your commenting toolbar. On the pull-down menu which appears, choose the very last item "Tool Default Properties...." A dialog box should open, On its tab "Appearance" click on "Border Color".
Did that do what you want?
I too run Acrobat 9 Pro. I just tested it and the change in default seems to persist after I close one document and open another, as you wanted.
Using Acrobat 9 Pro (9.4.7) in Vista —
Have the Properties bar open (View > Toolbars > Properties bar (Ctrl+E).
Place a Callout. Put focus on the text in the Callout. The Properties bar title changes to "Text Box Text Properties".
This toolbar permits changes to text color, text alignment, font (type, size) and application of bold, italic, underline, cross-out, superscript, & subscript.
Once the text color has been changed put focus on the Callout annotation's "box".
The Properties bar title changes to "Callout Properties".
Here, you can change the fill color, the annotation's border color, the line type and weight, & opacity.
Click on "More..." button to view the Callout Properties dialog.
Under the Appearance tab tick "Make Properties Default".
Changes made back in the "Text Box Text Properties" will become the default.
I changed the red text to blue. Saved & closed the PDF. Closed Acrobat. Restarted Acrobat & opened a PDF.
Applied a Callout and entered text. The text color was blue.
n.b., As Acrobat X is first fully Win7 "aware" Acrobat you may need to upgrade from Acrobat 9.
I know this is a really old thread, but I hope it notifies you that I found a potential fix. I was having the same issue and came here for help. I think I found a way to fix it.
Right click on Text Box Tool (should be adjacent to call out tool, its just the text box with border, no arrow), click tool default properties. The color of this might be the same as the callout tool. Change it to the color you want for the callout tool. save and close your pdf.
Open the pdf again and now do the same process for the callout tool. This should fix it. It did for me.
Now, never change the color again!