I managed to figure out why some software on my system simply refused to work (or even crashed) when using the SCIM input method scheme. It turns out I had upgraded my compiler for whatever reason and that was causing mismatches in the compiled code. Not terribly helpful really. I downgraded the compiler back to what came with the system (and, presumable, which the rest of the software on the system would have been compiled with) and rebuilt the SCIM stuff. Oddly enough, entering ひらがな (hiragana) characters is now a lot easier.
Theoretically, everything should now accept the new input scheme but you never know. Time will tell. Even so, it looks like everything I use on a regular basis is happy with the now compiler matched version of the SCIM software.