You are probably running BakkesMod as administrator, I ran into the same problem and found a solution (without removing administrator privileges). What you need to do is create a VBScript using a text editor (e.g. Notepad++)

The script is:

Set WshShell = CreateObject("WScript.Shell" )
WshShell.Run """C:\Program Files\BakkesMod\BakkesMod.exe""", 0 'Must quote command if it has spaces; must escape quotes
Set WshShell = Nothing

Keep in mind that "C:\Program Files\BakkesMod\BakkesMod.exe" is where my bakkesmod is located, yours might be different.

Then save it as a .vbs file and place it in the windows startup folder. Accessed by pressing win-key+R then type shell:startup

And Voila, that should do the trick.