How long was your bass without all four strings? You generally don't want to leave your strings off the bass for too long as it is the strings that help maintain the neck's tension. Also, are the strings the same type (brand, gauge) as the ones you had on before?
Don't hold me to it but those strings might be round cores. If so the core may be rattling around in the winding. Try removing the E and just near the top of the string where it goes into the tuner, put a little crimp in with wire cutters. Just enough to grip the core. When you put them back on, make sure they don't twist around too much and go on straight.
Don't hold me to it but those strings might be round cores. If so the core may be rattling around in the winding. Try removing the E and just near the top of the string where it goes into the tuner, put a little crimp in with wire cutters. Just enough to grip the core. When you put them back on, make sure they don't twist around too much and go on straight.