My startup disk does not stay set on OSX, rather it often reverts back to Mac OS 9.1 when I go into the startup disk control panel, even after having set it on OS X and clicked the padlock to lock it there.
In the startup disk control panel, the first OS that is found is darkened, but not selected, as it searches the system. The only way to actually select one is to click one it and maker sure that the text message has confirmed that you have selected the OS, otherwise the only thing that has happened is a search for OS's on your systems. This confuse my fiancee because she thought that it had selected OS 9.1, and she would restart and be back in OS X again. When I pointed out that she needed to click on her choice and see the additional text message, she didn't seem to have any further problems.
Here is a tutorial that explains how to boot into Mac OS 9.1 from Mac OS X. It mentions the problem that you discussed where a disk is highlighted but not selected and has screen shots that show the "You have selected..." message that you should look for to know what disk your Mac will boot next time you restart:
also, after you've highlighted the startupdisk, be sure to hit your "enter" key. when you do, you'll see the rainbow wheel spin. after its done, your choice is then "hardwired" for lack of a better term.
I have a similar problem. My main System is 8.6, and I also have 9.1 and OS X installed on separate partitions.
When I want to go from 8.6 to X, then I select the startup disk containing OS X (in Startup Disk), close it, and reboot. This brings up OS 9.1 all of the time. Then from 9.1 I can select X as my startup disk, and reboot. This will boot into X.
However, from OS X, I can select the disk with 8.6 and boot directly into it without going to 9.1 first. Strange.
Beige G3, 400 MHz, 512mB RAM, 10/20Gb HD, Firewire/USB, OS X 10.0.4