I was fighting thumbs problems for CR2 files for a while.
ANd yes, I gave up.
What I do is I run
ufraw-batch --embedded-image --out-path=./Thumbs ./*.CR2
It extract thumb embedded in RAW file to sub directory Thumbs. It substitutes solution but it run quickly and I am able to preview pictures and preselect them. I delete unwanted files. Then I run
ls ./Thumbs > z.pl #makes a file with list of pictures I want to process further
replace embedded.jpg CR2 <z.pl>z2.pl #prepare CR2 file list
rm ./Thumbs/* #wipe subfolder
cat z2.pl | xargs ufraw-batch --conf=MyConf --out-path=./PicsOK #generates jpg's from only selected CR2, put them to PicsOK
Notice --conf=MyConf - MyCOnf is a file with recipe how to process RAW files. You can change it according to specific conditions and pictures. What I do is I use interactive ufraw to find best parameters, just copy them to the file MyConf and voila.
Hope this can speed up you picture factory, as I did

Then I copy only CR2 that I want, and run
ufraw-batch --shrink=2 *.CR2
or rub interactive for files I want to make them better.
Since it is a quite a time, you probably find out. Ufraw is a command line but also interactive application for raw processing.
Intel® Sandybridge Desktop 64b Intel® Core™ i3-2120 CPU @ 3.30GHz × 4 MEM 3,8 GiB
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