My Stargate has the battery acid problem and it always resets each time it's powered on. If I don't hit the reset test button very quickly while the game powers up, it goes into that "50 ship/50 smartbomb" configuration automatically when I coin up the game. I can't tell the change has been made until you actually coin up.
I think it was done on purpose, so that the operators could play a 50 ship game and put up a crazy HS that everyone would try shooting for, then reset everything back to "normal". BTW I always play standard, factory 3 ship games. My HS is 188,000 but I can't prove it since it resets!