Dear Kenichi,
all IAST-letters work with IBus expect ~n. Usually if I write a '.' or a ';' then these letters are underlined because the input method recognizes these letters as special input letters, and waits for the next letter until the underline disappears. But if I write ~ then no underline appears at all. ITRANS seems to work fine.
I use bash. I tried m17n-edit again, and this time it worked better, the menus and the log-file (I don't know why it didn't work before). Here is the content of the log-file:
[IM] opening (sa IAST) ... ok
[IM] creating context (IAST sa) ... (shift init)
ok
[IM] [init] handle `input-focus-in' unhandled
[IM] [init] handle `ISO_Level3_Shift' unhandled
[IM] [init] handle `~' submap-found
[IM] [init] handle `n' submap-found map-actions: insert("ñ")
[IM] [init] (shift init)
(commit U+00F1)
[IM] [init] (produced U+00F1) [IM] destroying context (IAST sa) ... done
[IM] closing (IAST sa) ... done
Best wishes,
Christoph