Indeed, something has gone wrong, but it's difficult to put the finger on it, as such a thing never happened to me. So, let's start again from the beginning and take the
CubeX theme as an example :
1) After having unzip the
CubeX.ReaperThemeZip file, you should have find a
CubeX subfolder and a
CubeX.ReaperTheme file. Can you confirm this ?
2) In the
CubicPack3_ModPatch.zip, once unzipped, there are 10 files in the corresponding
CubeX folder : the 9 following files should have gone in the
CubeX subfolder in which there are all the graphic files, as well as the
rtconfig.txt one :
envcp_bgsel.png
envcp_hide.png
envcp_hide_ol.png
item_bg_sel.png
mcp_fxlist_empty.png
mcp_sendlist_empty.png
tcp_bgsel.png
tcp_idxbg_sel.png
rtconfig.txt
Among these 9 files, there is only one which is new :
envcp_hide_ol.png, which means that there should have been 8 replacements in the CubeX subfolder. Can you confirm this also ?
3) The last one is the
CubeX.ReaperTheme file which should replace the old one in the edited theme. So, at the end, are you sure that you have zipped TOGETHER the new
CubeX.ReaperTheme AND the
CubeX subfolder, change the extension of the resulting archive and put it back in the
\ColorThemes subfolder of your Reaper installation ?
If unsure, try again all the process with another copy of the theme. I don't have more time this evening (it's already 21:30 in France) but will come back tomorrow to see how things went. HTWH, though...