Rene, any luck with this?
I think it's extremely unlikely to be a permissions related thing. It would be very unusual to have config files in your home directory that are owned by root.
It's more likely that the files you mentioned are in use by other processes. So your backup software is either unable or unwilling to access the files to copy them.
Of the three config files you listed:
Enchant is a spell checker used by text editors/word processors. So if its config file is open, there must be a program/process running which is using the Enchant spell-checker. Shouldn't be too hard for you to work out which program/process that is. You probably had a text editor open when you ran your backup.
.gvfs is a config file used by the Gnome Virtual File System - If you are running Gnome, then it is almost certainly in use.
And dconf is another Gnome system component which stores settings and hardware information. So if you are running Gnome, this config file will almost certainly be in use too.
One way that you can verify that the files ARE open is to use the lsof command, which lists processes with open files.
If memory serves (At work ATM, so not on a Linux machine sadly), I think you can pass it a list of files and it will tell you what processes (if any) are using those files:
lsof /home/rene/.cache/dconf /home/rene/.config/enchant /home/rene/.gvfs
Else you could try filtering the output of lsof with grep:
lsof | grep '\.gvfs\|\.cache/dconf\|\.config/enchant'
You may or may not require sudo.... Again, been a while since I used lsof for anything, and I don't have a Linux machine handy right now.....
If any of the files are open (and they almost certainly are!) - In order for your backup program to be able to back them up, you will need to shut down the processes that are using the open files.
Shutting down the process which is using the enchant config should not present a problem. Once it is shut down, you should be able to back-up that config file.
But because .gvfs and .cache/dconf are config files for Gnome system components, I imagine that attempting to shut down the processes using those files would be a very bad and silly thing to do!
Offhand, the only safe option I can think of - if you REALLY want those files backed up; would be to boot into a LiveCD/LiveUSB of a distro which has some backup software installed on it. When you boot into a live environment, the config files on your HD will not be open. So you should be able to mount your HD and back up your entire home directory to your storage media.
I haven't been a Gnome user for a long time, so I don't really know the ins and outs of dconf or gvfs. There might be another way to back up their config from a running system..... Somebody else might have a better idea!