At compile time QDB saves SQLITE_VERSION_NUMBER (from the sqlite header);
at run-time it compares this to the sqlite library's version number.  If
it doesn't match, qdb exits.  So, fundamentally, you have a version
mis-match here.

Either:
  A) the sqlite header file qdb is being built against doesn't match the
sqlite library that you're building (perhaps you forgot to "make hinstall"
in lib/sqlite before building qdb); or
  B) qdb isn't using the libsqlite library you are putting on your target
(another library may be in the library search path).

To test for (B), you could start QDB with the DL_DEBUG environment
variable to determine where qdb is loading libsqlite from:
  DL_DEBUG=libs qdb -c ...

If qdb is loading the correct library then it's likely that (a) is the
problem and qdb is being built against a different sqlite header.

(As an aside: if you can, I would recommend using qnx-provided binaries
rather than binaries you've built yourself.)

-- 
Ryan J. Allen
QNX Software Systems