This certainly seems to be a system level issue based on what you've described, but I don't recall coming across anything similar. Based on the fact that MicroStation still recognizes them, I'm assuming that your drive mappings themselves haven't changed and that the current letters defined in your CFG files are still valid? Can you manually path out to the current locations by editing a currently defined variable? Also, it may be worthwhile installing Bentley Configuration Explorer to compare your MicroStation and ABD configurations to see how the higher level/parent variables are defined. I'd imagine this might be some type of "trickle down" effect where a few key variables are affecting everything downstream.
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