I suspect that the two fans included in your case must be connected to a PSU output. For that there is likely a connector somewhere that needs to be plugged in. Unfortunately the case Installation Manual does not discuss this point. What you're looking for could be either a 4-pin Molex male connector (about ¾" wide with 4 round pins inside a shroud) or a SATA power connector that looks like the wider power input connection on the back of a SATA drive. This would have to be plugged into a mating connector coming directly from the PSU so that you fans can get power to run. I suspect that your two fans do NOT plug directly into a mobo SYS_FAN header - is that correct?
Your mobo has only one SYS_FAN header, and one CPU_FAN header. They are both of the 4-pin style. For the BIOS screen to show you a speed on the SYS_FAN header, you would have to have plugged something into that header. Did you? What is plugged in there? Are you sure when you quote a speed of 1400 rpm that you are reporting the SYS_FAN, and not the CPU_FAN?
Let us know what fans are plugged in where, and we can advise further. Also tell us about the connectors on your two case fans - I suspect they are 3-pin female (with three holes in them) about 3/8" wide, but maybe not. In fact, if they are pre-installed and -wired into some case system, you may not be able to find those connectors.