Thanks to Mike Ashley from the Automator-users mailing list for the following code snippet that works around this:
on run {input, parameters}
set output to {}
repeat with i from 1 to length of input
set x to item i of input
set output to output & {quoted form of POSIX path of x}
end repeat
return output
end run
Just put a "do applescript" stage ahead of the "do shell script" stage, and put the above code in. It'll take the list of file aliases and convert them to properly quoted paths for the shell script to act on.
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