Yes, it doesn't seem quite right. Listening to my tape as a comparison, mine sounds "wide", and your's sounds "deep". I recorded raw MID/Side (as Left/Right) and mixed them to XY at home.
Some uneducated musings...
1) If you mixed MS mode on the fly with the Apogee, that creates XY type output, and you're done, right? No special decoding on the computer required.
2) If you had the cable +/-'s right, but mixed up the L/R cables=bottom/top=M/S, the M/S would be swapped into the Apogee, so instead of the apogee mixing "M-S=RightChannel", you would have "S-M=RightChannel". That would definitely be wierd, and would probably be like an XY with a phase swap.
3) Another possibility would be a mix up of the pattern switches on the body compared to the top and bottom caps. I know I get confused on the LSD2. i.e. you somehow had figure 8 front-to-back on the bottom cap instead of side-to-side on the top cap. It sounds awfully mono, which that would tend to do.
~~~~~~~~~~~~~~~~ 15 minutes later ~~~~~~~~~~
I don't think my idea #2 is correct. I just swapped my mid/side=L/R channels before running it through the MS decoder and it doesn't come out sounding like yours at all. In theory anyway, that would be a representation of that idea.