I found this:
In WinBox after opening the Terminal wondow, and pasteing a huge amount of commands, telnet and ssh stop responding correctly 
You can login… The ascii-draw Mikrotik shows… but no command prompt (huh bug in SH?:()… You cannot make any /system script…
Btw: It would be great to add /user active remove 
Also what about a RuterOS Bug Report Forum?
As always, you should make a supout file after this happens (if possible) and send it to suppout.
John
I have had the same problem…But I get round it by using putty to ssh in and paste the commands that way…
Putty also locks up after a while (about 500 or more commands) it looks like while adding the commands the CPU usage hits 100% and stays there and eventually it just cannot deal with more rules from the paste and they start failing. The CPU usage eventually stabilises back to normal but it does take a while…
Pasting 300 rules at a time works fine…
I found the same thing on a Routerboard 230 and a P233mmx system. I haven’t needed to paste that many rules into a more powerful box as yet…
How to make supout from winbox?
perhaps it will work writing a script and running it from winbox system/scripts ?
You cann’t… Let’s call mikrotik console as BASH SHELL… and it crashes… so you cann’t execute any command via telnet, ssh and/or script engine BLAH!!!
You can just reboot your router from winbox and everything is working again