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Question about using rockbox for audio and original firmware for video- ipod 5g

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GodEater:
You run it from your computer with your ipod attached.

Since you're using ubuntu, the command is not chkdsk - it's fsck.vfat.

mrufino1:
Thanks, if it happens again I will try that.
Does anyone have any advice on my question about which OS the ipod should be booted into when using itunes to transfer videos? I just need to know if having it booted in rockbox, then attaching it to my windows computer and using itunes is corrupting the rockbox file at all. Thanks for all of the help so far.

Chronon:
Rockbox has no USB mode.  When you make a USB connection to a computer Rockbox reboots into Apple's Disk Mode.  So, there's no fault of Rockbox as far as USB communication goes.  However, the USB mode within the Apple firmware seems to be quite a lot faster than that achieved in Disk Mode, so a lot of people prefer just to reboot into the Apple firmware when transferring lots of data.

As was suggested, a more likely culprit is removing the iPod from your system without properly unmounting, ejecting, etc.

mrufino1:
Well, a few minutes ago, more weird issues- I was out walking with my ipod, everything was fine, using rockbox with no problem. I got home, turned it off, put it on my shelf. I was reading the rockbox manual to learn more about themes, etc., and went to turn the ipod back on to start exploring a little. The ipod was not connected to the computer at any time today or yesterday and worked fine both days all in rockbox. Now, my font was again tiny. I went to browse the fonts, and it said there were no font files present. So I plugged the ipod into my linux laptop to check the folder, and it won't mount or even get recognized. I went to the command line, no indication the ipod is even connected. Strange. So I plugged into my windows laptop, ipod is recognized right away. I browsed the rockbox folder and the fonts folder, among others, is now renamed with very strange characters, empty squares and such.I  And there's more- windows will not let me access the rockbox folder to delete it, so I renamed the folder and unzipped a new rockbox folder on there. I still cannot delete the renamed folder, however, and now the computer  will not eject my ipod, saying it can't be stopped. What the heck is going on? Why are these files continually being correupted without being connected to a computer? The ipod works fine in ipod firmware, so I am not understanding what is the issue here. I DEFINITELY would rather use rockbox than the apple firmware. Thank you, sorry this has been dragging on so long.

EDIT: I was able to open itunes on the windows machine, eject the ipod, then I reconnected it to the linux computer and it is recognized.

SO:
The issue seems to be different from my original question about firmwares (which has now been answered with "It doesn't matter, it always goes to disk mode.", thank you for clarifying that). The issue seems to be, "Why is the rockbox folder being messed up without being connected to a computer?" As I said, files are being renamed in there. Replacing the folder seems to work, but I don't want to have to do this every day. Thanks again for all of the help so far, let me know if there is more info needed.

Chronon:
Have you run either chkdsk or fsck.vfat as was suggested?  This really sounds like filesystem corruption to me.  It's not surprising to me that it won't let you delete the folder/file.  Your file allocation table apparently contains invalid information and the OS therefore doesn't actually know where to find the data.  The problems will probably worsen if you do not fix them.  

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