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If you are using a Java version prior to 6.0, sufficient memory to run the thumbnails is not allocated. Try starting JIBS from the command line or a batch file with:
java -Xms500M -Xmx1000M -jar c:/ibs/JIBS.jar
The extra memory will cause the thumbnail cache to work better. Otherwise you may need to use a low row/column setting like 3x3.
You can rotate images in the thumbnail view and then save them. Image which have been rotated and not saved are marked with light green boxes in the upper left and lower right corners.