Open RA2.cfg, look for these four lines.
FSDisplayWidth=1024
FSDisplayHeight=768
FS3DDisplayWidth=1024
FS3DDisplayHeight=768
Change the numbers to match your monitor's screen resolution (For example, I changed "1024" to "1600" and "768" to "900") save and exit, then start RA2.
Not sure what I did wrong the first time to make it stretched out, but it seems to be working.