If you're in a hurry, just run Repair Database on Library B and try the import into Library A again. I have no idea why it's happening, but "Repair" is good and reliable, and if it fails that will be an important clue.
Did Kirby's suggestion work? Hopefully it did fix it.
If not, the version file inside the library bundle may be corrupted.
To fix this,
- Quit Aperture,
- Make a backup copy of your library "B"
- ctrl-click the libary "B" and select "Show Package Contents"
- In the folder that opens look for the folder "Aperture.aplib" and open it.
- Remove the file "DataModelVersion.plist" to the Desktop.
- Double click library "B" to launch Aperture. Aperture should now recreate the "DataModelVersion.plist" file. Edit one of the images a bit and switch to your library "A".
- Try to import again.