I'm not quite understanding what you are saying about the memory?
The problem with some older DOS applications is that you needed to have over 600k free lower memory. You'll not get that out of any DOS window operating under windows. Its tough to get that with the apropriate drivers loaded in a completely clean boot.
By the time you added the mouse driver, the vesa driver and any other minor drivers you needed, you sucked up the first 40k of lower memory.
I think the windows DOS boxes are starting at around 560k of free lower memory. You can type "Mem /C" to see just what they are doing... well.. maybe you can.
Another option is just to find an old DOS 6.2 system disk and boot from that. Good luck finding something that will work with today's MBs, USBs, ATA-100 and etc.
AKDejaVu