Keyboard input lost on desktop actions

If I change the name of a file on the desktop, I find that often this can result in complete loss of keyboard input as far as file names are concerned – i.e., it becomes impossible to change file names, name new files or make any keyboard input whatsoever. This can happen almost at once, or after an indeterminate number of file names have been changed; there seems to be no pattern or logic to the phenomenon. Suggestions?

I am having a hard time finding any common thread to this event. The last time it occurred, last night, I was running the following applications:
Firefox v 2.0.0.1
Entourage v 11
Word 2004 v 11
Photoshop CS v 8
Preview v 3.0.7
QuickTime v 7.1.3
Silverfast launcher v 2.1.2
Microtek Scanner Finder v 3.24
Otherwise:
Startup item: Microtek Scanner Finder v 3.24
APE extensions: Don't think any; I don't recognise the term.
Attachments: Printer (Epson Pro 3800), Scanner (Microtek i800), external hard drive, USB modem. However, I had these attachments even before the problem cropped up.
Finally, I have also run repairs and permissions corrections from Disk Utility without discovering any problems.
Many thanks for your help!

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    JMenuItem std = new JMenuItem("Standard");//creates menu item
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    JMenuItem helpTopics = new JMenuItem("Help Topics");//creates menu item
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