My guess is that the game cross-refrences it's resolution options with those that are supported by your monitor/driver (say when you go to display properties all the resolutions available on the slider) and just lists the ones in common.
If that is the case, if you use an Ati card you can try using Omega Drivers
here which are custom drivers pre-tweaked based on Ati's Catalyst (they also have Nvidia drivers but I can't really vouch for them). The neat thing about them is they give you a lot of options, one being something called multires which allows you to set virtualy any resolution imaginable between 320x200 and your native (and then some). Alternatley go to Display Settings>Advanced>"monitor" tab and uncheck the box that says "hide modes your monitor cannot display." Then you can see all the resolutions available though be carefull not to choose one that is out of your pixel range, it might damage your hardware.
Maybe seeing that your hardware is capable of displaying these will free up other resolutions in the game. Plus im sure omegas have more scaling options if needed.
The other thing you could do is force the in-game ws resolution through solutions found on this site, but i dont know if it will bode well for pillar-boxing.
Well those are my thoughts at least, btw what's your gfx and what games are you talking about?