Maybe there isn't enough stack for Iprefs. Too little stack caused problems with some AmigaOS 3.9 setups. You should probably check that you have these file versions...
IPrefs 45.13
setpatch 44.38
The SetPatch is important because it sets the stack higher for some tasks. Next you can try upping the stack with the stack command early in the S:Startup-Sequence before IPrefs but after SetPatch...
Stack 4096
This is not necessary on most AmigaOS 3.9 setups including mine. You might try the bug fixed AmigaOS 3.9 unofficial updates which add some stack to some modules that may be interacting with Iprefs. These also fix some bugs and I have been using without problems for quite some time. Info is here...
http://lilliput.host-cafe.com/start.htm