This about dosbox only(I run Linux so I do not really know what VDMS is)
You might want to make sure all the paths in the RESOURCE.CFG point correctly. Specifically that the drive letters match properly(and not on the computer-that they match how they have been mounted in dosbox). And it would not hurt to make sure that the directories have less than 8 letters. A good test from INSIDE dosbox would be to try going to that specific directory and see if you find anything.
And you should make sure the cd is mounted properly as well. It would be best to read the README file for instructions.
If you do not do it correctly, most Sierra games WILL NOT install from the cd(apparently because the program, if not mounted as read-only, will presume it has been already installed and try to work only using the cd, to much failure. Which fortunately in the event of an installation failure and a large enough hard drive usually gives the option of installing by simply copying the files onto the hard drive and altering their read-only attributes. Or for more advanced users, other options).
Also when I tried searching for your problem, someone else mentioned a possible solution (at least in dosbox) by removing the line 2
"if not "%0"=="CheckCD" goto Abort"
from the file CHECKCD.BAT. Though if your SQ6DOS.BAT has been altered to bypass the checks as you say, it should not be a problem.