Well, see a couple problems.

Shell "%COMSPEC% /C C:\kix\pkzipc.exe -extract C:\foldera\isafile.zip "$files" $folder\$file"

You got double-quotes embedded in double quotes, so get rid of those, plus your using the "$files" variable, instead of the $file variable, so maybe it would work better like this:

Shell ' %COMSPEC% /C C:\kix\pkzipc.exe -extract C:\foldera\isafile.zip "$file" "$folder\$file" '

-Shawn