If this happens to you, start FixMeStick again, and this time, when you see the message "FixMeStick starting in 8s. Hit any key for advanced boot options," hit any key. Then select the first Failsafe option.
Note: On Windows 8/8.1 and 10, a different message will appear at the bottom of the screen, not the top. This message is "The highlighted entry will be started automatically in 8s."
If the FixMeStick still does not start, please repeat the steps above and try the other Failsafe options.
If this still doesn't work for you, please create a support ticket so we can further look into the problem.