I would say this is due to the intonation. I have found this with my current bass. If you play around with harmonics, natural and artificial you can find pairs on different strings that are/should be the same pitch. If you find a few comparisons between strings that aren't always the same, try adjusting the intonation.
The paper under the saddles may have raised the string slightly causing the lnght of string that vibrates to change. I suggest carefully fiddling with the bridge but remembeing how many turns you have gone either way so if it gets worse you can always return the saddles to their original position.
This is my first reply so i hope its helpful. I still haven't got any replies
haha. Take care.