You mentioned that you just upgraded your motherboard? Was this the ONLY hardware change or are there other ‘new’ components in this system?
Is this a new (clean) installation of Win98SE after the motherboard upgrade? If not, I would suggest you start there — troubleshoot the OS first. Do a clean boot, nothing running from the STARTUP or REGISTRY –> RUN KEYS, see if it’s a device driver causing these lockups. Boot into SAFE MODE and get rid of all ORPHANED/UNKNOWN device objects. You may also want to go to all plain (default) BIOS settings while troubleshooting the OS install… once you are satisfied it’s not the OS, you can begin to tweak your BIOS settings back up to performance specs.
Also did you do this H/W upgrade yourself? Check all connections on the motherboard, and reseat the connectors and memory.
This is just a start to the troubleshooting required… but IMHO it is a good place to start.