First, go in and make sure it's in place properly.
Next, occasionally (though more and more rare these days) you have to pass memory size (in bytes) to lilo when it boots like so:
mem=134217728 (this would be 128mb in decimal form)
of course you can add this in lilo.conf as well under the particular install image for your kernel:
Still, your Linux kernel recognizing different amounts depending on the time of reboot may indicate a hardware problem of some sort.