What is non-congrouous?
 

During startup it said (reproduced from memory):

Booted 30 times without check.
Force check.
/dev/hda1 35/230 files 3.6% non congrigous
/dev/hda2 13/203 files 2.1% non congrigous
/dev/hda3 12/333 files...
.../dev/hda8 1/200 files 0.9% non congriguous

Does this mean that there are errors on the drive?
I thought it was supposed to only check ext2 type partitions?
I have /boot as ext2, plus 1 swap, the rest are all ext3.

I think that should be "non contiguous".
And I belive it means that the stated percentage of files are fragmented.
It is not an error, and you should not worry.

ext3 is simply ext2 with journalling, and as you have found, the filesystem will check itself automatically.

Remember the "Defragment Harddrive" program on Windows? The whole point of that program was to put your "fragmented" hard drive back together. Well on Linux the filesystems are a bit more advanced, so in some cases fragmentation still occurs, but its self correcting. Not to mention, if I remember correctly, you need atleast 5-10% fragmentation for it to really effect anything, i.e. performance.