Sorry to sound like a broken record but I've come across another couple of limitations that have stopped me dead in my tracks.
At the moment it looks like you can't use one variable to set another one.
I set up an event like this
Modify-variable
-Variable1 (Value 1)
-Variable2 (Value 2)
(You'll have to type in @Variable2[Value 2] to get the second one to work BTW)but it doesn't assign "Value 2" to Variable1 (

it just sets Variable1 to 0 for some reason).
This wouldn't be so bad if I could assign an argument to the variable but it won't let me do that.
Modify-variable
-Variable1 (Value 1)
- < argument >
Simply assigns the string < argument > rather than assigning the value of < argument >
Sorry to sound like I'm moaning about this but this is fast becoming my favourite feature in FRED. I took a sprawling MG mission and managed to stick the contents of about 12 complicated SEXPs in to one single every-time-argument with it but that's all for nothing if I can't assign one variable from another.
I've included a short mission you can use for testing (so as to save you making your own from scratch).
I'm also encountering an intermittant lock sometimes when I try to create a new modify-variable SEXP. Not quite certain what is causing it though. It only locks after I've created the SEXP and clicked on okay to close the Events editor. I'll try and pin down what causes it.