I see that at times using unetbootin, generally with a message to unplug and then plug in the usb again which almost always works. Try that.

With regard to the Chakra iso on the flash, as has been pointed out above, this is a read-only (iso9660) filesystem and you can't change/delete files on it. Any changes you make will not be available on reboot. That is it's nature. You have two basic options; use some method (dd, unetbootin, etc.) to overwrite or format the two partitions. You could also create a new MBR on the device. Make sure you get the correct device. You can use GParted, which you said you have, to do all these things.

UNetbootin expects the USB flash drive to have a partition formatted FAT32 and otherwise empty. You do not copy the ISO file to the flash drive beforehand. UNetbootin copies the files from the ISO image (either from the network, or a file somewhere on your system) to the flash drive and then sets up the boot loader.