Hi Christian,
I have the same problem and just found my solution:
I use the MFG Tool to set the OTP Bits. The MFG Tool also has some flaws in 64bit environments (when clicking on Options->Configurations->USBport the program crashes, so just don't click there), but it works well enough to burn the OTP bits.
In the MFGtool/Profiles directory you have to define a new profile (I just copied an existing one, replaced the .sb file with OtpInit.sb and modified the ucl.xml File. The following posting describes what has to be modified:
How to set OTP bits with MfgTool?
This is the contents of my ucl.xml file
<UCL>
<CFG>
<STATE name="Recovery" dev="IMX28"/>
<STATE name="Updater" dev="Updater" />
<DEV name="IMX28" vid="15A2" pid="004F"/>
<DEV name="Updater" vid="066F" pid="37FF" />
</CFG>
<LIST name="Singlechip NAND" desc="Install on singlechip NAND">
<CMD type="boot" body="Recovery" file="OtpInit.sb" timeout="60">flashing OTP.</CMD>
<CMD type="burn"/>
</LIST>
<LIST name="SD(with uboot)" desc="Install to SD card">
<CMD type="boot" body="Recovery" file="OtpInit.sb" timeout="60">flashing OTP.</CMD>
<CMD type="burn"/>
</LIST>
<LIST name="SD(without uboot)" desc="Install to SD card">
<CMD type="boot" body="Recovery" file="OtpInit.sb" timeout="60">flashing OTP.</CMD>
<CMD type="burn"/>
</LIST>
</UCL>
I'm pretty sure that my .xml file is not the optimal solution (most likely it is no necessary to write the command 4 times), but I tried this and it worked.
I hope this can help you.
Best regards,
Christopher