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Open up a terminal and start "top" to see if there hung or zombie processes while you are processing your images. There may be a call or pipe that's hanging and it takes a while for it to clear.
Also, look into the system logs (via either viewing the files directly under /var/log or by issuing the dmesg command).
You should be able to get clues as to what is causing the program to stall or lag.
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