Alrighty...this is definitely odd. I tried saving without making any edits, like you suggested, and it saved just fine, so I tried making the changes again. Lo and behold, now it magically works perfectly. :shrug:
It sounds like a parsing problem to me. Most of the time, when the script can't "compile" (aka doesn't recognize one or more commands), it will tell you that when you try to save the script. But, it's possible to save the scrpt with some commands or edits that will then make the CS crash when you try to save the whole mod.
I had the exact same thing happen to me recently. It took a long time, but I traced it back to using two eval commands (an OBSE function) on the same IF statement. It turns out that eval was never meant to be used twice in the same command, but even so I was able to save the script before saving the mod caused a crash.
Another common reason for the CS to crash: having a SET statement that's too lengthy.