Notes On Intonation

Getting the fat strings to come in to proper intonation can be problematic.

This isn't a manufacturer-specific problem. It's an electric bass problem that has its roots in how the strings "flow" (for lack of a better description) over the saddles. New strings do not "break" properly over the saddles, which leaves you with strings that vary their tension due to a curve near the saddles.

Before I dive into this, a little posterior covering is in order: YMMV. The procedure below assumes that the bass in question is well built and properly assembled. It also assumes strings that are new or in good condition.

Put on a fresh set of strings and tune them to pitch. Don't do anything else - just tune them to normal pitch. Now look at the bridge edge-on from the fat string side. What you'll probably see are the strings curving over the saddles in a nice & pretty arc. The strings come up from the back of the bridge, or from the bridge plate, make a kind of lazy change of direction over the saddles, and head off up the neck. The curve over the saddle actually continues for an inch or so on the neck side. The curve may be slight or marked, depending on your strings (flats seem to do this more than rounds), and will be more noticeable on the fat string. Setting a straightedge on the fat string will make this readily apparent. That pretty curve will make stable tuning difficult. It may also make intonation nearly impossible to set with any accuracy and stability, or without some extreme settings on the intonation screws. This isn't what we want, so let's try to fix it.
Because the skinny string will likely have very little curve compared to the others and will be bent into a mostly angled break over its saddle, we can figure that it's very close to what we're after. So let's adjust its intonation using the usual method; open & 12th.
Now adjust the intonation screws on the remaining saddles so that the saddles are set in an angled line with the fat string's saddle about 1/4" to 3/8" closer to the butt end of the bass than the skinny string's saddle. As you look down on the body from the butt end of the bass, the fat string's saddle would be a little closer to you. This should give you a rough intonation setting once you complete the steps below. Don't adjust saddle height - only intonation.
Re-tune all strings to pitch.
For each string, even the skinny one, place your thumb on the string just to the neck side of the saddle and press straight down toward the body fairly hard. Look at the bridge edge-on again and you should see that the pretty curve is now a sharp break over the saddle. That's what we want! If any of that curve remains on any strings (different strings may need more of a push than others), press on them again.
Check tuning and you'll probably find that all the strings will be flat in varying amounts. Re-tune to pitch.
Now check your intonation on all strings. You should find that, even with eyeball adjusted intomation, the strings aren't too far off. Adjust as needed to bring them into proper intonation then press on each string one more time. Re-check tuning and intonation, re-adjust if necessary, and you should be good to go. If you have a saddle lock screw, don't forget to tighten it.

BTW - our friend Chef gave this procedure a term. It's called "Reinforcing the witness point". I like that. Makes it sound scientific.