Safe Mode bypasses config.sys, most of autoexec.bat, and the regular startup list.
1. start-run-msconfig....look at config and autoexec to see if there are special settings that need to be used or don't need to be there. I see this when upgraded from W3.1 or W95, or when install floppies are used for CD/DVD drives or other things. You could try using "selective startup" and unchecking all sub entries, which is almost like safe mode. Find the free utility ASviewer, autostart viewer, standalone, which will list a whole lot that initiates with Windows, and it will be a shorter list than regular startup.
2. Your PC may have non-standard mobo, processor, chipset that need special drivers-settings to fire up. Safe Mode uses generic and fail-safe drivers for minimum load. Video-modem-sound card won't be initiated. CD drives won't be availible unless CDEX stuff is in autoexec for DOS mode use. Make sure there is no CD or floppy in a drive.
I would guess there is a device trying to initiate and won't, or something trying to initiate that is stopped from doing so in regular startup. Obviously, the whine is a fan under stress or the processor maxed out.
A more un-regular area would be "setup" or BIOS, checking for entries that may cause trouble.
3. get, update, and use AdawareSE and Spybot Search and Destroy, some use Spyware Blaster and Spysweeper (trial-pay). Usually this crap will mess up regular boot, not safe mode, but who knows. Many people have "malware" and don't know it.
4. Haven't run into this duck. Usually it's a lockup, BSOD, or reboot. Another way to try safe mode is to let Windows start loading and shut off PC prematurly. On restart "windows did not finish loading on previous attempt, use Safe Mode...." and you'll see the option again.
5. how have you been getting to safe mode? F8 or ctrl and then the menu?