Emulator

What steps will reproduce the problem?

1. Go to Config, set "HLE the IPL"
2. close Dolphin
3. check Dolphin.ini: HLE_BS2 is set to True, so far this is correct
4. start Dolphin
   5a. either go to Config, "HLE the IPL" is now unset
   5b. or close Dolphin straigt away and check Dolphin.ini again,
   HLE_BS2 is now False

What is the expected output? What do you see instead?
I expect the option to stay enabled when I enable it, even beyond several Dolphin restarts. If this option is meant to be disabled regardless, I expect there not being such an option.
Instead, I see it getting unset at each Dolphin start.

Dolphin version with the problem? Other Dolphin version without the
problem?
with the problem: r5768, r5769
without the problem: r5767 and before

32-bit or 64-bit and any other build parameters?
x64, lint=True, all other parameters at their default

OS version and versions of tools/libraries used?
Debian squeeze

Please provide any additional information below.
I have the same problem with Dolphin r5769 on Windows 7 Professional x64.