I’m a proud owner of an Amiga 1200 with an internal 4GB CF ide hd and an external 2GB CF to exchange stuff with my PC. Because the initial setup wasn’t that good I reinstalled the system with 3 partitions and installed the Classic Amiga Workbench.
All games went on partition 2 and 3 for using with WHDLoad. Most games work fine but I wonder why certain games work from the external CF card but not from the internal. After some searching I found out that it might be worth to check the MaxTransfer setting of the partition as the scsi.device driver in the original version (40.12 on my setup) only works fine with certain values.
I used the Harddisk Installation Tool to do this:

1) Select the desired drive and press “Partition drive…”

2) Select a partition and press “Edit Partition…”

3) Click into the field MaxTransfer and change it to 0x1FE00 (Why?)

4) Press “Use”, then “Use” again and finally “Save changes to drive…”

Note: You have to do this for all partitions of the selected drive.

After this changes I didn’t noticed problems anymore. So far, so good 🙂

Useful links:
http://en.wikipedia.org/wiki/Amiga_Fast_File_System
http://hjohn.home.xs4all.nl/SFS/maxtrans.htm