I've only skimmed this thread, but I didn't see this mentioned. There has been some changes to DBD::SQLite at version 1.10. From the current pod:

unicode

If set to a true value, DBD::SQLite will turn the UTF-8 flag on for all text strings coming out of the database. For more details on the UTF-8 flag see perlunicode. The default is for the UTF-8 flag to be turned off.

The Changes file says:

1.10
    - Fix Unicode support (DOMQ)
[download]

So with luck all you need is an upgrade