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Digging into the source code, this fatal error line only appears in SQLiteProcedures.cc if the variable ok is set to false. Above this line, ok is initialized to true, and then followed by series of 5 if checks that can reset ok to false and result in the fatal error you are seeing. The order of these checks are:

• Test if EnergyPlus can write to the SQLite error file
• Test if EnergyPlus can create a new SQLite file
• Test if EnergyPlus can write to the SQLite file
• Test if the SQLite file is locked
• Open the SQLite file so that EnergyPlus can write simulation outputs to it

I would recommend opening the SQL file after a failed run to search for any error messages. You can open this in a text editor, but it would be easier to navigate in a database GUI. A free tool like sqliteman, or a free trial of a commercial tool like RazorSQL are some options.

@Kyle Benne seems to be the last person to alter this source code, maybe he can chime in. It is definitely interesting that just by running the same IDF a number of times, this fatal error eventually goes away on its own. I'm guessing that for the initial runs that fail, the SQLite file is locked or EnergyPlus cannot open it.