Hi Frank,
Thanks for taking time. (I'm on the same project)
"The strange thing is every environment has been setup in the same way, but this only happens at this Development server. SQL has been setup case insensitive, so that shouldn't do this magic." - Wono
Besides what he mentioned at first and to answer your question: The prefix is equal on both systems.
Settings -> system settings -> customization:
Prefix = 'Cm'
Example = 'cm_entity'
There's a Capital 'C' in the prefix, but you can't do anything about that. MS CRM auto-capitalizes the first char of the field. When making customizations the 'cm' is used as prefix.
We still don't have a clue how one customization.xml is differently handled by two similary setted up MS CRM installations...
More ideas?