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I have the later model mac mini as well with HDMi running 10.6.6 Mac OS and XBMC 10.0-RC2 R35567. I have the mac mini routed to a denon receiver as well for HDMI switching and outputted to a samsung LCD TV. I have two profiles setup - one for the TV and one for my projector - this requires individual calibration profiles within XBMC. I have not had any issues with xbmc losing the calibration settings in either profile.
In the mac settings, i have the output set to 1080i - are you able to use 1080i resolution with your setup?
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**UPDATE**
I lined up a Finder window in the bottom left corner of my plasma and then proceeded to switch HDMI sources back and forth. Low and behold, that Finder window shifted around randomly, just like the Video Calibration in XBMC. I must not have noticed it previously because of the default overscan.
I also installed Windows 7 x64 and the same exact thing happens.
So it must be an issue where the HDMI syncs itself to a random position with my 1365 x 768 plasma. This position varies from 3 pixels in width to as much as 11 pixels in width horizontally and/or vertically. I can only assume that the non 1:1 pixel mapping with what the mini is outputting (either 720p or 1080i) is causing this issue to occur.
For now, setting the Mac mini to output 1080i combined with setting a good amount of overscan in the XBMC Video Calibration minimizes the problem.
I'm hoping this won't occur on a 1080p plasma since it will be 1:1 pixel mapping.