I've almost got the same problem as you do with my HP ProLiant server on the latest BIOS update the SLIC 2.1 it's definitely there but disabled and I don't know how I can enable it without replacing or using Yen's method. The SLP 1.0 is there but SLIC 2.1 isn't. If I flash with a older version it has SLIC 2.0 and that shows up with the SLIC dumper but I want 2.1 and I had problems activating server 2008 with the SLIC 2.0 and a cert I generated that apparently matches. I would like it also if I could just enable it rather than have either 2 there with the old one renamed as SLAC or replacing it. Which tool did you use to flash your BIOS once you used Yen's method I've already tried flashing from my .ROM dump with PH161700.EXE /X /FORCE /O /C /S and it just caused the computer to beep 3 times and poped up with an error, I was told that I should rename the BIOS to a shorter filename though did you have to do that or did you just leave it as the default the tool creates? Did you use PH161700.EXE?
I flashed the BIOS with WinPhlash under a Windows PE 3.0 environment [Windows 7 install USB flash drive]. I've done it numerous times and have had absolutely no problems. Can you provide a link for the modified BIOS and an unmodified one? If you don't mind. Also, a SLIC dump from the SLIC 2.0 enabled BIOS.