This definitely sounds like something not related to the DX50 or SD cards causing problems...software, driver (usb controller?) or OS related most likely, but I'm not discounting hardware problems because it's still a possibility. It's quite a simple process, as you should only need to drag the files onto the card like any other external media. If something is causing a conflict in the file transfer (either some piece of software or OS corruption), then my first suggestion to rule that out is to try a different computer. You can also try booting in safe-mode before you begin transferring to rule out any software driver conflicts. I think the suggestions for using an external card reader is because there may be an issue with the built-in card reader on your laptop, but if I had to guess I'd say it's software related based on how you describe the problem. I have likely the same Sandisk 64GB mSD card (30mbs transfer speed estimated, got on Amazon) and when I filled it up recently after reformatting (full transfer of about 59GB) it took no more than 2 hours IIRC.
So, try reformatting the mSD card again, reboot in safe-mode and see if you can successfully transfer the files. If that doesn't work, try it on another machine. Also you may want to see if you are able to copy over other types of files to see if you get the same issues. If you continue to have issues, then perhaps there is something wrong with the files themselves?
Now that I'm thinking about it, does anyone know if the Mango firmware 1.2.8 accepts all types of FLAC/ALAC, or is there a limitation regarding bit depth (16bit vs 24bit) or something along those lines? I primarily use Rockbox now, but I don't have any 24-bit FLAC files to test myself...though according to the specs there should be no issue with this. What I'm guessing is if the computer says the files are on the SD card or they are visibly there, but the DX50 can't identify them for some reason due to tags, format incompatibility or corruption...not sure if anyone else experienced this before.