Yes, I'd expect what you got.
First of all, I'm intrigued that you found a way to connect a 2-pin fan to a mobo fan port. All mobo fan ports I've seen for some time are either 3- or 4-pin in a particular arrangement of pins with a plastic tongue sticking up next to them. This is to ensure that the female connector from the fan wires fits onto it only one way. On the other hand, the only "2-pin" fans I have seen are those that have only 2 wires from the fan motor, but actually have a large male "4-pin Molex" connector on the end, to mate with an output connector from the PSU. That fan connector could not fit a mobo fan port. So, either you (or someone) custom-fitted a fan with a new connector (or used an adapter), or you have a very different fan entirely.
Anyway, irrespective of connectors, the wiring connections would have to be correct. Both 3- and 4-pin mobo fan ports provide the Ground connection on Pin #1, and +VDC on Pin #2. On a 3-pin port, the voltage on Pin #2 varies from 0 to +12 VDC. On a 4-pin port, that voltage is always +12 VDC. Your fan would have to connect to these two pins. IF you were to connect them in reverse, the fan would turn but in the wrong direction.
But here's the big problem that likely explains your non-functioning system. That fan you describe with "2 pins" obviously does NOT have a third wire to Pin #3. In 3- and 4-pin fans, this wire carries a pulse train signal from the motor back to the mobo for speed measurement. You plugged this fan into a CPU_FAN port. MANY mobos have by default (you can turn it off in BIOS Setup) a system on that CPU_FAN port to check the speed of that fan constantly. Of course, it is assumed that the fan plugged in here will be the real CPU cooler! If that fan ever fails to send a speed pulse signal to the port (which is what you created, OP) the system assumes that the CPU cooler has failed and initiates an immediate safety shut-down. First it sends out a warning beep on the mobo mini-speaker (PZO) and a message on the screen, then it shuts down the whole system. This is all to prevent the CPU from overheating and being destroyed for lack of cooling. This system does not even wait for the normal CPU temperature sensor to signal high CPU internal temperature. On a start-up, the warning sound and screen message may not last long before shut-down happens.
For people who have such a protection system in their mobos' CPU_FAN control system but who want to cool their CPU with some fan that is NOT connected to the CPU_FAN port (and hence will not supply the speed signal to that port), the BIOS Setup screens allow you to tell it to ignore that system. So you lose one extra CPU overheating monitor that way, but you system will run.
By the way, OP, since you do not know the origins of that fan, examine it very carefully. Look particularly for voltage and amperage specs on it. If it came from some very different application, it may not work the way common computer case ventilation fans do. Common fans operate on 12VDC (max) and consume typically 0.3 to 1.0 amps. Really high-performance fans for computer cases still use 12 VDC, but may consume up to 3 or 4 amps, and no mobo fan port can supply that.
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