Why did i ask this? 'Cause i experienced a different "behaviour" of the moho windows formation, depending on different resolutions:
1280x1024

1024x768

960x529

848x480

800x600

720x576

720x480

640x480

For me it works best with 1024x768.
Nevertheless, after i rearrange the windows and open moho again, the windows keep the rearranged formation, AS LONG AS I DON'T GO BELOW 1024x768.
Maybe for your two monitors there is another "key-resolution" possible.
So i suggest to test it yourself.
I don't have much to do with dual monitoring, but afaik you need a software to get dual monitors work together. Right?
So maybe that's what causes the trouble?