@leirbag28:
You may not notice any errors right away with a 3GB hard drive if partitioned in such a way that there is one partition larger than 2GB, however go ahead and try to partition your new 40GB hard drive with OS3.1 and see what happens.
If you try to create a partition larger than 2GB, what HDToolBox does in OS3.1 is start to overwrite from begining of the drive space after crossing the 2GB partition barrier.
Trust me, there is no way OS3.1 can use more than 4GB of your drive space. You must upgrade to at least OS3.5 to avoid this problem, or get a better filesystem.
I suggest upgrading to OS3.9 as it is miles ahead of 3.1.