I've read somewhere that writing files directly to a cf-card over the network is bugged. That could be the same problem.
It might work if you put em temporarily on a sd-card, internal memory or usb-stick and then move them from there to the cf-card. A bit of a roundabout way but it might solve your problem until you have a new cardreader.
I've moved files around a few times with mrxvt and that doesn't seem to cause problems.
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