The size doesn't really matter in ms3d, you can still use the $scale command in the .qc to resize it in the compiling process.
Oh, and I'd like to help you more, but unfortunately you seem to use ms3d 1.7.x because I cannot open it. Could you please zip up the reference smd and attach it so I can have a look?
Oh, and for glass cubes I suggest to make the walls thinner.
You created the cubes in a wrong way. Have a look at this sketch:

And now here I got a step-by-step instruction on how to create that structure.
1) Create a box
2) Select that box (the faces of it, not only the vertexes!), and hit CTRL+D. You won't see a difference but you just dublicated that box!
3) Do not unselect it! Instead, just switch to the "Scale" option and change all 3 axis' values to about 0.95. Then hit the "Scale" button right next to these boxes again and again until the inner box has the correct size.
4) While still having the faces selected, hit "CTRL+SHIFT+F", followed by a "CTRL+M". The first command turned the faces around, so that the inner box' walls face inwards and are visible from the inside. The second command updated the smoothing according to welded vertexes and the smoothing groups, but that is not important right now, as you only have 2 boxes.
5) After the "CTRL+M", if the smoothing gets somehow corrupted (you will notice strange "shadows" on the formerly bald faces in the 3D window) just select all vertexes of both boxes and hit "CTRL+SHIFT+W". This unwelds the vertexes, and another "CTRL+M" will show the bald sides again.
This is only a quick fix and not suitable for more complex models. As a start, you may try to assign the boxes' sides that are connected to DIFFERENT smoothing groups, this will fix the smoothing as well.
Don't forget "CTRL+M" when assigning faces to a new group. here are plenty of smoothing group tutorials out there which are easy to understand, so you better try to read them because even thes best model can be ruined by miserable smoothing.
6) Now you have 2 boxes inside each other, and the visable edges are reduces to a minimum. If you want the model to be open to one side, do the following:
7) Select all faces on one side of the 2 boxes, let's say the faces facing upwards on the upper ends of the boxes. To select only them, just select all faces but then deselect all the other faces by doing a "Shift+R-Click" select on the vertexes on the other end.
8) Delete those faces! Now the 2 boxes will be open to one end, but you can see into the gap between the walls! Oh noes! So let's hurry to
9) The creation of a good looking opening.
10) First off, select the vertexes of the inner box that are closest to the opening. Now, go to the "Move" tab and deselect the X and the Z axis. This requires that you created the opening at the top of the boxes!
Having only the Y axis selected will elimate any strange placement of vertexes because you can only move them into one direction. This is a very important element of ms3d! Get used to it

11) Pull the vertexes you selected up, until they are at the height of the outer box' top vertexes. Make sure that the gap is as small as possible, or you will lose the square-sided character of teh outer box!
12) Now select the outer box' top vertexes AS WELL and hit "CTRL+SHIFT-Y", which will equal those vertexes' Y level and create a 100% perfect plaing surface.
13) Not select the box' LOWER vertexes and hit "CTRL+H", which will hide the, ("CTRL+SHIFT-H" unhides everything btw). Being unable to select thos vertexes is important for the next step.
14) Go to a 2D window with "Top View". Now, use the "Face" tool to select those vertexes and to close the "gap" between the boxes.
15) You create faces by clicking on 3 vertexes after each other. The face created will face TOWARDS the point of view you created them in when you selected them in COUNTER-CLOCKWISE order. Backwards=Clockwise. Keep that in mind!
16) Fill up the gaps. Done!
Steps 7) - 12)

Steps 13) - 16)

Attachment: Example model created this way. Be sure to check out the smoothing groups!