If you have divided your components into groups and then do the whole 'group replica place' and 'copy trace' thing, you have really nice identical groups. If you want to arrange these groups into a nice matrix layout then you can't use the Align functions without first going 'Edit - Group Selection'. Then it works perfectly. But if you do this, then the next time you forward annotate ultiboard thinks that these components are not on the board and needs to be placed again.
It's not a major bug, you can just go 'Edit - UnGroup Selection' after you've placed them but I still thought you should know about it.
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/Peter Hygren