I never had such problems: No color changes ever happened to me. You are probably not using it correctly - see explanation below.
I think I was using mask without realising about that alpha effect.
In both clip and mask, you select two objects, and after applying clip or mask the result is that the lower object is clipped or masked by the upper one.
Okay - thanks. That helps. Also, I found an option in the settings to leave the original clip object - which really helps one understand what's happening. Still, that's another diff to Freehand. With Inkscape's approach, there are now two objects - whereas with Paste-Inside there was only one object, as expected. Now, internally the picture may be different, but from the user pov, there was just one. In Freehand, if you wanted to hide the parent object, you simply gave it no outline.
In clip, it is constrained to the shape of the upper object, regardless of the upper object's color/opacity/blur properties.
Cool. Is there any way to interactively move the clipped objects around and see the effect live? Unsetting all the time is rather unfriendly.
With mask, it is also influenced by the upper object's color like masks in photoshop or Gimp or Illustrator: Where there is a white color in the upper object, the lower will be opaque, and where there is black, it will be transparent.
I did not know this until your email. There is no hint in the help files. Cool feature. I tried it out. It's kind of odd though. I found it very tricky to change the fill of the mask so that the opacity of the children could be tweaked. Again, it was a matter of: Unset - Change - Select - Set - Repeat.
Am I doing it wrong?
AFAIK In 0.45 (and perhaps current test versions) you will be able to do it, but you need to be in outline mode to see the clip or mask object.
That's another of my pet peeves - outline mode is also weird! :) It only shows the current selection in outlines - everything else is still normal with fills etc. This makes it impossible to use really. Am I missing something?
Talking about pet-peeves - don't get me started on stamping! :D
Thanks for the feedback!
/d