i think the pq magic boot menu would still work, as you seem to be having pqmagic 6 and i think just add the linux native partiton to the boot menu and it might help.
If it does not why dont you use loadlin to boot into linux. just create a batch file in dos so that you dont have to type in the command again and again and just excute the batch file when ever you want to connect to linux. "loadlin c:\vmlinuz root =/dev/hdax " where you need to copy both loadlin and vmlinuz to c drive or any other drive and set the parameters in the above command and hdax is the linux native partion.
another option (not tried this one) is to set lilo to use linear addressing in /etc/lilo.conf which might probably get rid of that 1024 limit, but read the lilo docs before trying this out.