I don't see anywhere in the spec where Fout duty cycle is specified. The output pulse will be narrow and inverted. I don't think your allowing enough time for the output to settle. You can try ramping up the power supply over a few milliseconds.
If you want 50% duty cycle, I think you'll have to add a flip flop to the output and operate at half frequency or double the operating frequency. Its been awhile, but I have an LM331 on hand and guess I can build the VtoF again to verify.
Meanwhile, try this:
I've outlined the changes below.
1. I replaced C1 with an X7R cap over the existing one. The existing one had missing params. This is for the sim only...in real HW use a temperature stable cap like an NPO.
2. Removed "startup" directive. But now have to add IC statements.