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Thank you very much for joining the Intel® Rapid Storage Technology communities.
In regard to your question, remember that every time that the SATA mode is changed on the BIOS the installation of Windows from scratch is necessary, because it will not boot if you change the SATA mode after the installation was completed and if it does like in this case some devices might not be properly recognized by the tool.
On the following link you will find the IRST version that should be fully compatible with your system, please try to install it if you are currently using a different one:
If you changed SATA mode to “Raid” and if you try to access the control + I menu, are all the hard drives showing in there?
The Intel® RST is a very reliable tool, it consumes more resources because it is an external application, as you mentioned it does not belong to the operating system, which is why it is also more secure and safe since it was build specifically to provide that function.
Please let me know the results of trying the steps above.
Any further questions, please let me know.