Not sure what you mean. I could not find a setting for a "base clock" by name. I didn't change any BIOS settings other than POWER ON after loss of power. Plus, I set the date and time. Since I build so many NUCs, I try to make as few BIOS changes as possible. Keeping it simple! In fact, I have never even updated a NUC BIOS out of the box until this one.
In the NUC it would show as "Host clock frequency" and you would find it in the advance tab=> performance=> processors. Please check this setting, it should be at 100.
I used that Intel Processor Diagnostic Tool on this same model NUC and it failed the base clock as well, this would not be a problem with the NUC but rather with the tool, it is just not reading the processor information properly. I already sent this matter to the engineers to check the tool.
Out of curiosity, I downloaded the IPDT_Installer_18.104.22.168.W-2_x86_22.214.171.124.W.MP-1_x64 tool and ran it on my completerly up to date (BIOS and Drivers) NUC5i7RYH. It too fails only at at different point. My box passes everything supported until it hits the platform controller hub test.
--- Error while retrieving SATA Device Information from OS ---
..Platform Controller Hub Test Failed..
Platform Controller Hub Test Failed. Error while retrieving SATA Device Information from OS
--- Test End Time: 06/19/2015 15:34:18---
Processor Name: Intel(R) Core(TM) i7-5557U CPU @ 3.10GHz
Processor Information: Intel64 Family 6 Model 61 Stepping 4
Number of Physical Cores: 2
Number of Logical Cores: 4
Installed System Memory: 16 GB
Operating System: Microsoft Windows 8.1 Pro 64-bit
Graphics Information: Intel(R) Iris(TM) Graphics 6100
System Product: NUC5I7RYB
System BIOS: RYBDWi35.86A.0249.2015.0529.1640
Thought you might be like to know.
I decided to edit the test settings. Started by changing the BaseClock tolerance from default (5%) to 6%. Failed. Increased to 7%. Failed. Increased to 8%. Failed. Increased to 9%. Failed. Increased to 10%. Passed.
Then I went backwards, from 10%, to 9%, then 8%, then 7%, then 6%, then 5%. All Failed.
Went back up again and it failed at 10%, 11%, 12% and 13%, Stopped there.
Funny thing is, the clock (which should be 100) is testing at 107, so 7% or 8% should pass.
Very inconsistent results with this particular test.
I finally had a few moments to research my small and, possibly off-topic, contribution to this discussion. Apparently, there are a few known issues with the Platform Controller Hub architecture that have been around for a long while and show up from time to time in the diagnostic software. One of these is an inability to detect some SATA 6Gbit/s devices. In my NUC 5i7RYH, I'm using a 250GB CriuciaL Drive (232GB Crucial_CT250MX200SSD1 (SSD)) and a Transcend 256gb(238GB TS256GMTS800 (SSD)) which work perfectly well but were not detected by the latest IPDT (IPDT_Installer_126.96.36.199.W-2_x86_188.8.131.52.W.MP-1_x64(1)). I downloaded, installed and ran the test a second time to eliminate the possibility of a corrupt installation. I got the same results as those I previously reported.