There seems to be a number of potential issues here.
First of all: filesize and bitrate is no indicator of audio quality. Many SACD/DSD sources do not contain high resolution audio - they're just converted from a CD master.
Secondly: you cannot compare SACD conversions to a CD rip. It's entirely possible that they are sourced from different masters.
Thirdly: why go from DSD to 352.8kHz WAV to 44.1kHz FLAC? Media Center can do the conversion directly.
I don't have access to a Mac right now, but on Windows at least, Media Center does the conversion correctly.
Make sure that Media Center is properly configured for it though:
- Tools > Options > Audio > Settings > Use SoX for Resampling
- Tools > Options > Audio > Advanced > Dither Mode: TPDF Dither.
- Enable DSP, and make sure that the only option you have selected is Output Format in DSP Studio (set to stereo 44.1kHz).
- Set the bit-depth to 16-bit.
- Set the FLAC Encoder to Verify Encoding.
Now Media Center should be configured to convert directly from DSD to 16/44 FLACs.
One tool you can use to check the encoded files is
Spek.
If the FLAC file is lossless, it will either have data extending to 22.05kHz
or natural looking peaks. If it's sourced from an MP3, it will have a hard cut-off at 16kHz.
I had to go through three different SACD albums before I found a clear example like that though - the other two discs didn't have frequency information that even went up to 22kHz.
Posting the result here may be useful.