This seems to be a Reaper problem, so the best will be to contact the Reaper developers.
A workaround would be to give HALion the complete control over the key-commands by opening a new GUI window drawn by HALion and not by Reaper.
- To do that load HALion by “Insert virtual instrument on new track…”
- Click on “open new window” (see picture below)
- select “All Editors (Advanced)”
- done
best regards
Gerrit Junge