So far we could find out a bit more:
First, the line has to be extremely long. While mIRC processes lines of more than 1k characters without any problem, the crash occurs in a line with 3,400+ characters. The whole crashing line we want to process (excerpt from a German weblog) can be found here:
test.txt (Too long for pasting here directly, sorry.)
One more thing we noticed:
If we just
//echo the replaced line without using a %var, it works. The crash only happens if we try to assign it to a variable. This thing is getting stranger every day. :-)
(Using /tokenize instead of a var works, too, so obviously the variable assignment is broken here.)
To make it easier to test, I changed and added the code from above to a new script file:
test.mrc 
