I got a bass tuned down to C# with some Steve Harris Sig. Rotos, and this is my first time using flats. The bass was playing pretty good after some saddle adjustments. Now it's about two months later and I'm getting some fret buzz towards the headstock on the middle strings. I thought I read somewhere that flats sort of sag/lower when they break in... or did my neck just move?
It might be the neck need adjusting to the change in tension. When you changed the string set and switched to C# tuning have you adjusted your truss Rod? Just an idea.