To disable the master password prompt you have to specifiy a file containing the password with -eclipse.password, see Eclipse SDK Help and Bug 241223.
The complete procedure is as follows (this is on Linux, on Windows it should work as well if you change the paths):
Exit Eclipse Delete the directory ~/.eclipse/org.eclipse.equinox.security Create a text file containing your master password, e.g. echo "secret" > ~/.eclipse/master Add to the very top of eclipse.ini, found in the Eclipse program directory (as two lines, don't combine into one)
-eclipse.password /home/user/.eclipse/master Start Eclipse again.