Has boeing changed their alarm systems post that incident?
The story of Helios Airways flight 522 is complicated. It is not clear that a misidentified alarm was the cause of the crash.
If you are talking about the cabin altitude warning horn, that was allegedly misidentified as a take-off configuration, then nothing has been changed, at least up to May 2015 (see: The Boeing 737 Technical Guide, Version 70, May 2015, bottom of the page 50).
"As the aircraft climbed, the pressure inside the cabin gradually decreased. As it passed through an altitude of 12,040 feet (3,670 m), the cabin altitude warning horn sounded. The warning should have prompted the crew to stop climbing, but it was misidentified by the crew as a take-off configuration warning, which signals that the aircraft is not ready for take-off, and can only sound on the ground.
In the next few minutes, several warning lights on the overhead panel in the cockpit illuminated. One or both of the equipment cooling warning lights came on to indicate low airflow through the cooling fans (a result of the decreased air density), accompanied by the master caution light. The passenger oxygen light illuminated when, at an altitude of approximately 18,000 feet (5,500 m), the oxygen masks in the passenger cabin automatically deployed."m, Source: Helios Airways Flight 522.