This is a common symptom of a failure to cache the additional memory. The exact problem depends on your motherboard.
Sometimes you have to enable caching of certain regions in your BIOS setup. Look in the CMOS setup and see if there is an option to cache the new memory area which is currently switched off. This is apparently most common on a '486.
Sometimes the RAM has to be in certain sockets to be cached.
Sometimes you have to set jumpers to enable caching.
Some motherboards don't cache all of the RAM if you have more RAM per amount of cache than the hardware expects. Usually a full 256K cache will solve this problem.
If in doubt, check the manual. If you still can't fix it because the documentation is inadequate, you might like to post a message to comp.os.linux.hardware giving all of the details—make, model number, date code, etc., so other Linux users can avoid it.