I've tried to execute the following "Helper" as a login item under "Users & Groups" > "Login Items" hoping this would fix the MS mouse issue under El Capitan - This did not work.
/Library/PreferencePanes/Microsoft\ Mouse.prefPane/Contents/Resources/MicrosoftMouseHelper.app/Contents/MacOS/Micro softMouseHelper
What did work & still works reliably is that I created a shell script and crontab entry using "Terminal". The script is as follows. Note that your Microsoft Mouse Helper file name may be named differently so ensure you find the correct one, should be same or similar.
######################################
# file name : /users/myloginid/mouse
######################################
#!/bin/ksh
# The following red text is one line in the script, the forum just wraps the text.
nohup /Library/PreferencePanes/
Microsoft\ Mouse.prefPane/Contents/Resources/MicrosoftMouseHelper.app/
Contents/MacOS/MicrosoftMouseHelper > /dev/null 2>&1 &
exit
# Set execute permissions on the file.
chmod 755 /users/myloginid/mouse
# Create a crontab with one line as shown. This gets executed when the system boots.
crontab -e
@reboot /Users/myloginid/mouse
:wq!
# View the crontab
crontab -l
@reboot /Users/myloginid/mouse
Now reboot the Mac and see if your mouse is working right.
This has been working reliably for me without disabling SIP with csrutil.
Randy