Interesting, let's diagnose your issue a bit if possible. This is the first we've seen this reported in this forum AFAIK, but 2.50 was released not long ago, on 7/22. Plus things can be missed for a long time before being noticed, as we saw recently. Hopefully something is not wrong the the board, such as the CMOS chip itself, although that can be replaced pretty easily if necessary.
What method did you use to change to 2.50, Instant Flash, DOS, or Windows?
I know you don't or can't change all the options in the BIOS (example, you use RAID mode/RAID array so can't change to AHCI), but does it seem like the same options all the time that won't be saved, or just random? Are the options all related to the CPU or on one page or screen of the BIOS?
Changing certain options will cause the board to shut off and restart (BCLK Ratio for example), that is normal, but those options are rare. If the board shut off after changing a fan speed configuration, something is wrong.
A bad battery in the board can cause strange things to happen to the CMOS chip and BIOS options. Mother board batteries can be goofy, I have a four year old board with the original battery that works fine, and I've had to replace batteries in boards that were a month old. I can't say your battery is bad, just something to keep in mind.
A BIOS can reset some options if they cause the system to crash on start up, like setting the memory speed to high, timings to fast, etc, depending on the BIOS. Not saying that is your situation, since you would know you had a restart of the PC after changing options like this.
I've seen in my ASRock board's BIOS, that changing one option will automatically change others. For example, changing the CPU core multipliers to values in the mid 40's will cause the CPU Input Voltage to be set higher. The CPU fan speed profile may be changed to High Performance or Full On as well. It's may be possible that you choose a value for an option that causes others to change, and then change the first option back again, but the other(s) don't get reset as they should. Just reviewing some of the possibilities before we decide that the BIOS is not saving values, rather than it seems not to be saving them due to the behavior I described.
Have you ever used the BIOS profiles option, where you save all the settings in a profile that can be restored later? That should be in the Tools section. Saving your settings just before clicking Save and Exit would be a good way to confirm that the settings changed spontaneously. You just click Load for the profile, and check if the setting changed back to what you think it should be.
Any chance that you are using A-Tuning in Windows, and applying things like fan speed settings in it is changing the corresponding BIOS options?