|I just realized that I didn't really answer the question:|
The settings are stored in the registry under:
Custom(relating to title)
There is the possibility that the current settings are part of a shortcut......
it's possible to also create a key with <screentitle>(your choice) populate the desired entries that differ from the default and shell out a new console/cmd with 'start "<screentitle>"'.
The reg entries for buffer and window size are DWORD's so you would need to bit shift with set /a and convert the result to hex and then use "reg" to add the values.
Edit: Here is an example of getting the dword - it would still need to be converted to hex:
rem 100 cols
rem 200 lines
set /a "(200 << 16) + 100 "
Stupid me of course you could just set up the values you want as string because it won't need to change.
In my testing on xp setting a window value higher than the system max caused the max to be used instead which is a win.
There is still always the issue of the registry being restricted......