The transistor "generates" a voltage drop of about 0.7 volts, and so does the diode.
(What's the reason for the presence of that diode ?)
This is why i said you added a couple of diodes to the switch (a transistor can more or less be seen as a controllable diode).
This effect allone will mess up your setup, and will show a difference between switching with a switch and with a transistor.
Just don't beleive what you're being told, measure and see what's going on.
If you want to be sure to replace the switch with something you can control with an Arduino or whatever, use that transistor to switch a relay.