Multiple Versions Problem-Two of each track in one album

I have a large number of multi-disc sets that were issued in HDCD. I ripped them in dBpoweramp with and without HDCD decoding and in some cases using two different HDCD settings. I use my own naming conventions, such as putting the HDCD version, and sometimes the Disc number, in the album title in brackets like [HDCD] and [HDCD-6]. I have selected all the albums and set the tagging to use my album titles and not Roon’s. (I know this is not the preferred way of dealing with box sets but there is no way I am reorganizing all the folders involved.) Usually this works but for a number of albums Roon combines the two versions in a single album with two of each track. (It also shows multiple discs in the set, which is correct in a sense but not what I want as I include the disc number in the title and want each shown as a separate album.) In those cases Roon also ignores the names I gave the albums and uses its own and does not display on the album cover the information I put in brackets. For other albums it works just the way I want. How do I fix this and keep my own organization scheme? I have “show hidden albums” selected in the General tab.