My apologies if this has already been noted, I did not see anything with a basic search. The BPI-R3 schematic shows pin 3 ( fan_pwm ) of the 3-pin fan connector ( CN23 ) is tied to the 3.3V rail ( VDD33 ) through a 10K resistor ( R321 ) acting as a pull-up for the PWM line. While I realize this is not designed to comply with standards ( 4-Wire Pulse Width Modulation (PWM) Controlled Fans”, Intel Corporation September 2005, revision 1.3 ) as this is using a 3 pin connection for PWM rather than the specified 4, using a 3.3V pull-up for the PWM line electrically conflicts with the standard and can be seen on the board.
The fan that comes in many of the R3 kits has an internal pull-up resistor connected to its PWM line ( as most any PWM fan will ), this pulls the line up to 5V. This can be measured with the PWM pin removed from the connector, plugging the connector in and checking static voltage on the removed wire. By the schematics, this is placing 5V power onto the 3.3V rail. How much this changes the 3.3V rail voltage will depend on where in the circuit you measure, as any resistors in the 3.3V circuit become voltage dividers, and will create different voltage zones between them.
I would suggest removing R321, or if it’s felt having this pull-up is required due to the modified pinout of the connector, adding a diode to prevent back feed from the fan side, for future designs.