Inline HDCD decoding is only done on the original 16 bit file, whether in wav format or a lossless format like flac or alac.
If you have "24 bit" HDCD source material it's already been converted by another decoder, in theory you get about 20 bits of resolution in a 24 bit sample.
You don't want to manually mark the files as HDCD. MC will determine whether or not the source material is HDCD. The default value for that field is -1 when the material hasn't been scanned to see if it's HDCD yet.
You can test the HDCD detection by changing the HDCD tag for a track to -1 then right-clicking on the file and do audio analysis (unclicking the skip analyzed files option) then do the audio analysis look at the value for HDCD at the far right of the analysis window. It will now be either 0 or 1.
If you have a track you are CERTAIN is HDCD and you do this test and MC doesn't think so, I'd like to get a copy of that track to test. If it's small you can email it to me at bob (at) jriver (dot) com or use something like firefox send to get the track to me. Thanks.
I'm a little confused on the first section of your post so let me say this, and go from there....
I rip CD's in APE format using dBpoweramp. The rip program has a DSP filter you can set to detect HDCD's upon ripping. Once the filter is set if dBpoweramp rips a CD that is HDCD encoded, you will be notified as shown in the attachment. That CD will then show up in JRiver as 24-bit CD (attached image), with an HDCD code of 0. If I "Analyze" the CD, the HDCD code either stays at 0 or (for some CD's) changes to 1. If changed to 1, when playing a track off the disc, I'll get "HDCD and says Process HDCD enabled, but bit depth is wrong" This is tested with "known" HDCD disks!
So the short of it, I use dBpoweramp to rip which detects HDCD's and rips them as such. Those CD's show up in JRiver as 24-bit CD's, but will say they are the wrong bit if played in HDCD decoding. These are known HDCD's.
And I did the HDCD detection test on the known (as in written on the CD) HDCD disks and 3 of the 4 changed from -1 to 1, while the other moved to 0. Odd. Nonetheless, 24-bit, still say wrong bit depth. That said, no sound issues or defects.