File Name Bubble Hovering on Screen

I can't say much about preventing this, but there is no need to reboot. Just kill Finder, using Force Quit from the apple menu or killall Finder in a Terminal window. A new Finder will then be started in the old one's place.

Any file or folder that begins with '.' is going to be hidden in the Finder. That has always been true, back to the days of NeXTStep.

If what you are trying to do is automatically rename files that begin with a '.' to not begin with a '.' that can easily be accomplished with a shell script. Save the following as /usr/local/bin/rename-dot-files.sh:

#!/bin/zsh -f

DIR="$HOME/Downloads/"

cd "$DIR"

ls -1Ad \.* | egrep -v '.DS_Store|.localized' | while read line
do

        NEWNAME=$(echo "$line" | sed 's#^\.##g')

        /bin/mv -vn "$line" "$NEWNAME"

done

exit 0

That script will look in $HOME/Downloads/ for any files that start with a . (excluding .DS_Store and .localized which you do not want to rename) and will rename it to the same name, without the '.' as long as there is no other file/folder with that same name.

To do this automatically you will need to create a launchd plist that will automatically launch any time the directory changes:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>Disabled</key>
    <false/>
    <key>Label</key>
    <string>com.tjluoma.rename-dot-files</string>
    <key>Program</key>
    <string>/usr/local/bin/rename-dot-files.sh</string>
    <key>RunAtLoad</key>
    <true/>
    <key>WatchPaths</key>
    <array>
        <string>/Users/luomat/Downloads/</string>
    </array>
</dict>
</plist>

Obviously you'll want to change the path from /Users/luomat/ to whatever your $HOME is.

Save that plist to ~/Library/LaunchAgents/com.tjluoma.rename-dot-files.plist and then load it as:

launchctl load ~/Library/LaunchAgents/com.tjluoma.rename-dot-files.plist

The script will run whenever the ~/Downloads/ is changed, which includes any files being added or removed, but it automatically limits itself to files which begin with '.'