What version of the system is it? A IIci needs at least 6.0.4 to run.
It could be that the startup disk was made for a particular Mac model. If you made it for, say, a Plus, it will only work on a Plus. Try using an original disk or use one of Apple's disks from their site (I'd use either the 7.0.1 disk tools floppy or the 6.0.8 System Startup disk).