Are you 100% certain you have the correct ROMs? Core functionality of the PCMCIA slot comes from a module in the Kickstart - A1200 and A600 ROMs have it, the others don't. If you accidentally bought/burned/received 3000/4000(T) ROMs, that might explain why the PCMCIA slot isn't working anymore. Another possibility is that you've got a combination of ROM- and disk-based modules that are conflicting - did you write the correct (i.e., A1200) modules ADF to disk?
The system will append .1 to device names if there are identically-named devices connected to the system. Does everything look normal in HDToolBox? (i.e., you didn't accidentally duplicate your partitions.) This could be another Kickstart module issue, like the system somehow ended up loading 2 copies of scsi.device. Confirm with SysInfo, Scout or a similar utility - you'll see scsi.device and 2nd.scsi.device if this is what's happened. You can also confirm with HDToolBox - set the tooltype to use 2nd.scsi.device instead of scsi.device. If it works and you see your drive/partitions, then you've got a duplicate.
The next diagnostic step for the duplicate devices is to go to the Early Startup Control menu from a cold boot. If the duplicates are showing up then, then it's a module issue in the ROMs. If they're only showing up in Early Startup after a warm boot, then it's a module issue on disk.
Bottom line, something seems off with your Kickstart. You may want to revert to Kickstart 3.1 and go for a fully disk-based installation of 3.2. That will eliminate the physical 3.2 ROMs as a possible problem at the expense of some RAM and a slower initial boot. You shouldn't need to nuke the drive, but may need to run the installation again to ensure all the correct disk-based Kickstart modules get onto your hard drive.
