How are you trying to do this?
Two things NOT to do:
-DON'T do this with old strings, new ones only. And be sure you have correctly installed the strings on the machine-head pegs. I've rarely seen a complaint of 'This ^$^@^#&@ guitar won't stay in tune / tune up' where the strings on the pegs didn't look like a bowl of spaghetti. 'I NEVER cut them', those idiot loops of string, or those sharp ends sticking up in the air . . . . come back when you grow up, please !
-DON'T do this with the axe laying on its' back, do this sitting down with the bass across your lap in playing position.
The saddles should move back and forth along the string length, I would not expect to have to raise or lower the bridge in total to synch your string length to the scale, i.e., 'intonate' your bass. If you look closely, each saddle in the bridge is resting on a threaded rod which terminates in an allen-screw cap at one end. Insert the right-size Allen wrench and turn (you may have to de-tune a bit to lessen the downforce/tension on that screw, then re-tune to check the new position) and the saddle will traverse left or right depending on which way you turn the wrench. If you're using anywhere near normal gauges, at some point your fretted 12th fret note and the 12th fret harmonic will match exactly, and you're done. Repeat until all the strings are done. On an older axe, a drop of good lubricant on the threads (not WD40 ! !) is not a bad idea.
Raising or lowering the bridge is a crude way to sharp or flat your tuning overall by a few cents, the idea behind those fine-tuning tailpieces Gibson used on their solid bodies, but not a way to intonate your bass, generally.
Joey
