intonation out...heavy gauge strings to blame?

[lauralowbass]

Hello! I play a 5 string fender jazz bass but cannot get the bottom string to behave. The saddle wont go any further back on that B string and yet the string still gets sharp past the 7th fret. The strings on it at the mo are nickel round wound heavy gauge (50 - 125 I think, the bottom string is not any heavier than regular 5 string set's bottom string would be though, could heavier G - E strings affect the bottom B strings intonation?) and when I got the bass it had regular guage strings on it and I didnt notice any problems, I think the heavy strings have upset it a bit over time since I put them on 4 months ago. I have heard that the gauge of string affects intonation, I was wondering if any of you encountered heavy gauge strings causing intonation problems? I have tried all the other things I can think of, string heights, even tweaked the truss rod etc to get it set up perfectly and its lovely but that bottom string just wont cooperate!
Please share your intonation experiences with me, I hope someone else out there has been through this and can confirm my wonderings before I go out, buy new strings and set it up all over again!
Thank you

[ThePerfectBass]

You may have a bad B string... I don't think I've ever tried a set of strings that would not intonate... That being said, I generally opt for a .125 low B. Maybe try another B string of the same gauge, brand and model and see if it works before making a complete setup change.

Peace!

[NYCbassist]

Sorry if this is a little late but...I have definitely had basses run out of adjustment. I have been able to fix it by using different string gauges. I believe a slightly smaller gauge will go flatter as you go up the neck. I am working on a bass right now that required me to move the bridge. But, I used a reg. scale neck on a long scale body. Try a thinner b string. GL