It's the dialog generated by the PDF printer. The one that says now printing page 1...2...3...etc. It appears centered on the monitor, and when VS goes to grab the screenshot for the PDF, that dialog is centered on the map, thereby causing it to be in the finished PDF file.
icebear77, I have asked Zzzzz, the creator of VirtualScape, and his answer is
here.
In short, the best and fastest way to fix the problem is to render your map in 3D and print from the 3D screen. Let me know if it works

.
That problem still occurs, but if I grab the dialog quick enough to drag it off the screen, it works fine. I just have to be quick.
Thanks for assisting me. Maybe Zzzz will get it fixed in the next release.
I was having the same problem as icebear77 and the answer given in the link from Longheroscaper wasn't working for me so I kept plugging away at it and I came up with something that did work for me.
Windows XP:
-Select the "Start" button
-Open "Printers & Faxes"
-Right click on "CutePDF Writer"
-Select "Properties"
-Select "Advanced"
-Select "Print directly to the printer" radio button (This should uncheck "Spool print doc. so program finishes printing faster")
-Select "Apply" button
-Select "OK" button
Note: This will effectively freeze the printer prompt windows in place allowing you time to move them before the program takes a snap shot of your image for the PDF.
VirtualScape: (Have both the 2D window and 3D image window open)
-Select "File"
-Select "Print"
-Select "CutePDF Writer" from the drop-down box if it isn't already.
-Select "OK" button
*The "Save As" window will appear -
DO NOTHING at this time
except drag the window to the side.
**Take the "VirtualScape" window that was behind the "Save As" window & move it completely off the screen.
***Minimize the VirtualScape program window.
****
NOW, go back to the "Save As" window, enter a file name, and select "Save".
Your new PDF has now been created, saved, and, hopefully, without any unwanted windows in the middle of your images. If the VS part doesn't work the first time, try it again. Every once in a while it doesn't take the first time for some reason. I hope this helped.