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I was trying to implement simple AC-compressor switching in FSIO. No such luck. Even the simplest of expressions don't seem to do anything. Latest Firmware (20180729 1812).
I tried the following:
set_fsio_output_pin 3 pe5
set_fsio_output_frequency 3 0
set_fsio_expression 3 "rpm > 3000"

I get positive feedback in the console log, the expression gets translated to RPN and everything. If I don't set an expression, I get a recurring error. It's clearly trying to work.
I also tried lots of other variations, I tried different pins- no result. Even checking the pins on the brainboard directly- nothing.
VVT control also doesn't seem to want to change any actual PWM setting. I can see in the console and debug fields that it's trying to do something, but there's no output to hardware.

Any idea what I'm doing wrong?

One thing I forgot to mention: Fuel Pump, which -I believe- uses FSIO, works just fine.

fsioinfo shows that you are somewhat close.

if RPM above 3000
2018-08-01 07_53: EngineState: FSIO #3 [rpm 3000 >] at PE5@0Hz value=1.00
if RPM below 3000
2018-08-01 07_54: EngineState: FSIO #3 [rpm 3000 >] at PE5@0Hz value=0.00

So looks like things are not bad on the firmware layer, open question electrical layer. Did you writeconfig and reboot ECU? set_fsio_output_pin command is not smart enough to apply pin selection on the fly.

https://github.com/rusefi/rusefi/issues/601 created. Message added as a temporary measure - https://github.com/rusefi/rusefi/commit/af1c64712b791e76d0c7635e965d10abf2cfd834

Ooops. No writeconfig. Did a bunch of re-boots though. Will try tonight.
I also still have the open question how to actually reference an input pin in a formula. My attempts using "input 1" and "input_pin 1" seem to have failed.

So- writeconfig and reboot seem to be really helpful in getting FSIO to work. Thanks!

I am glad we have progress! Sorry for making it confusing - at least there is a message now, some little progress. Hope to make this better once I have time, we have a ticket so request would not be forgotten.