To find out the version of your MMD, go to (assuming you have the English version) Help, and then About. It should display a small box with all information about your program.
I know that some models come in the PMX format, and they should open in the newer versions...perhaps you have an older version. My version is 7.39 (the DirectX9 version on the official website) - it's not the newest, but it's reliable. I have yet to get the 64bitOS version myself.
These files are accessory files (.x) and open through Accessory Manipulation (it's the yellow section). I don't understand how accessory files would be affected by the inability to load PMX but hey, I didn't make the effect nor MMD, so of course my overall knowledge is limited.