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I've had a quick look at the "bulk extract" and there is a memory leak issue going on. However it is inside the Calibre code in the converters (non-pdf) as far as I can tell - certainly extracting from LRF files (which is horribly slow) the leak is pretty nasty and noticeable.
I'm sure at some point Kovid and co may take a look into this - in the meantime stick to extracting ISBN from small batches at a time and you will be fine. The other option I have is to run the extraction in separate worker processes like bulk conversions do. It would be a little slower probably but at least this problem should disappear and the GUI hopefully wouldn't choke every now and then like it does currently.
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