Ye, but then again: It's the fault of the user: Not necessarily the program.
I love Joes SS-er, because it's about as safe as going on to the neoboards. It all depends on the list you use, 95% of the time. Though I avoid potatoe counter bigtime, since that has always been the one to freeze me: No matter what score.
And if I don't know the mods, I personally have the GM script that can SS 2, and shows what mods you use, the times, etc. So it's perfect to build lists as well.
Even trophies should be safe enough: As long as you make it look like someone has been playing for real.