Hi all, and thanks for your replies! Formatting the SD card in the camera with low-level format did the tricks, so now it's back to 8GB!
Also, sorry for my late reply. I wrote the post in a hurry before leaving for a festival this weekend, so I didn't have time to write all the info.
I have an old Canon SD850IS from 2008 that I use with CHDK in order to get a little more out of the photos. I've used to have CHDK on a single 8GB partition, but I thought I'd try to use two partitions so I could have it start automatically. But I think I'll just stick with the solution I used before (I know, if it ain't broken, don't fix it..
).