The following's from this post I had going over in General Windows Support, and I thought it'd be more useful here, so im pasting it now into beta...

well, ive discovered some new behavior in 4.1.10....
unlike previous versions, when i install or re-install 4.1.10 it will add the startup entry into the startup folder. ( I haven't looked at the shortcut properties, tho), but if I move the reg entry from common startup to either HKLM/HKCU startup i see the checkbox stays checked in lw, and whether or not i delete each and every startup entry relating to lw, regardless of which HK its in, LW won't put the shortcut into common startup via the checkbox unless I reinstall. And whats worse... Once i move the entry from common startup to either HK, the start in tray switch doesnt survive. So ive tried via batch again, and something's wrong.... These are some ive tried:
A. start /abovenormal limewire.exe /startup -min /min -startup
B. start /abovenormal limewire.exe -startup /startup -min /min
C. start /abovenormal limewire.exe -startup
D. start /abovenormal limewire.exe
...and this is what happens:
A. & D. starts the splash screen way
B. & C. command window closes without launching the exe

....so now im off to reinstall for the 5th time.... grrr

The startup behaviour hasn't changed since it was introduced (a while ago). It's always been the case that you need to either re-install LimeWire again or drop a link to LimeWire in the startup folder (and add a -startup parameter to the command) in order to do a startup, in addition to checking 'Start On Startup' in the options in LimeWire. Yes, it's clunky, but we didn't have an easy way of making a link to start LimeWire through Java. At some point we'll come up with a better way of doing it, but it's not really a huge priority now.

ugh that means its all my machine.... god sometimes i really hate windows