For caching a minimal amount of information, AmigaOS uses what is called "buffers" on all forms of disks - floppies and hard drives. A certain number of them, which is adjustable, are allocated during bootup. There are two possibilities for your problem:
1) The hard drive has a lot of buffers configured via the respective parameter in the RDB. Use HDToolBox to reduce that buffers number for each partition. This is not likely in your case because the amount of memory in use changes when you use different install disks.
2) The non-Commodore install disk is using the "AddBuffers" command to add a large amount of buffers to the hard disk device name. On that install disk, check the S/startup-sequence file or the S/user-startup file for the "AddBuffers" command. Reduce the number after it to reduce the amount of memory that's used by the HD.
