Do you lose your map flags too? Because if so, you need to back up your ryzom/save/interface_<yourname>.icfg file. Here's a script I use to do it every time I start. I then run the script instead of Ryzom directly, of course. You should change the third line if you didn't install Ryzom to /opt:Then if you find your windows moved and map flags gone, quit Ryzom and replace your interface_<name>.icfg files from the backup.
#!/bin/bash
# Ryzom likes to find the default config in the directory it's run from.
cd /opt/ryzom
# If the client crashes or is shut down without a chance to save, you lose
# some settings.
date=$(date +"%Y%m%d %H-%M")
echo "Will be backing up to $PWD/$date"
mkdir -p "backup/$date"
cp save/*.icfg save/*.xml save/*.pack save/log_*.txt "backup/$date"
cd backup
tar -cjf "$date".tbz2 "$date" && rm -r "$date"
cd ..
./ryzom_client