Here is a basic short term fix... assume your 'server' is on root of c: and is called 'world'
BAT FILE:
:START
c:
cd\
cd server
del world\data\ICL-worlds.dat
launch.bat
:END
I'm sure you can write a cleaner script (my real one also includes a backup routine) just run that bat file instead of the tekkit one, it will run tekkit for you.
The end result of this is your server won't crash, but you will have to re visit each anchor manually to activate it - a new ICL-worlds.dat gets created.