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Intonation still off - can't make strings any longer

Thicker strings will bring a stronger magnetic pull from the pickups which could lead to a warbling/ intonation problems in the upper regions of the neck. Try lowering your pickups slightly.
 
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Welcome to TB. You may want to try putting your bass back the way it was with the rounds on it. Provided the strings weren't hopelessly dead and unable to tune, this will give you a reference point. Check to see if everything is in working order (especially truss rod adjustment) and how much neck relief there is. Once you've satisfied yourself that there is nothing seriously wrong with the instrument, try the new setup again. It sounds like a combination of things are the cause. Heavy flats have much more tension that lighter rounds, so they tend to pull on the neck more, that means you must adjust the truss rod to compensate, the silk wrap should never go beyond the saddles where it can influence the string height at the bridge. One often overlooked hidden cause of problems can be loose neck bolts, make sure they're tight. There are many intelligent members here at TB who are always willing to help. Listen to these guys, they know what they're talking about.
 
Thank you to everyone for this incredible education. You showed me a few problems with the way I was approaching this adjustment.

I didn't set the witness points. I checked the neck relief last night and the neck is being bowed significantly by the greater tension of the heavy flatwounds. I did not file the nut when I switched to heavier strings.

I looked up the Ibanez manual for the 1993 SR400 and it seems that the factory adjusted them for 100 gauge E strings. So now it's really obvious that I needed a complete readjustment.

So I will start from the beginning and go through all the steps, and possibly find a luthier. I really appreciate all the advice here!

Thanks again!

Peter
 
Press on the string on both sides of the nut and saddles at the same time, firmly. You want the string to go straight from tuner to nut, then straight from nut to saddle. Also, the heavier strings may need to be pressed to the tuner post as well, to make them straight to the nut. It'll save on wear to the nut, and will stay in tune quicker.
 
Don't file the nut unless its necessary, if the larger string will fully seat into the slot without binding then there is no reason to file it. Unless the action at the nut is high.
 
I had one of the new Rotos without the silk on the ends not intonate properly because it kept binding in the saddle slot. Since you have silk on the saddle, that could be getting hung up. I would give up and go back to the same gauge rounds that were on it before. That's what I did, problem solved.
 
With your advice and help from a luthier, I fixed the problem. I'll describe it here in case someone reads the thread later on.

I took the bass to a luthier and he tightened the truss rod as far as it would go. He told me that the neck was still too flexible to resist the tension of the heavy gauge strings. We could not get the bow out of the neck with those heavy strings on it.

I checked the Ibanez manual for the bass (SR800 actually) and it said the factory set up was for strings with a 100 gauge E string. So my 110 set was much heavier.

Back at home, I switched to flatwound DR medium gauge strings (45 - 105) and checked the neck relief again. With the truss rod still as tight as possible (where the luthier left it), the medium strings had a much lower action. They were almost playable, but buzzing on the first and second frets. So I loosened the truss rod about a quarter turn and checked the relief again. At that point, there was about 1/32" of clearance at the first fret. That's less than I hoped for but I left the truss rod alone anyway. The action is low, the strings play extremely easily, and I am not having problems with fret buzz.

With the low action, I was able to adjust the intonation perfectly. The saddles are back to the middle of their adjustment range.

So I think the answer is that a 22-year old bass with a thin and flexible neck (feels great for playing) is not strong enough to handle Rotosound flatwounds (50 75 95 110). Reducing the string gauge and tightening the truss rod set the bass up perfectly again.

Thanks for all the help and advice. I learned a lot!

Peter
 

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