I would use FS-UAE, much newer code. But that's really odd, depending on which version of kickstart you're using, the NTSC vs PAL shouldn't matter. Though it may on the older versions. Personally, I'd probably always just run in PAL, I do on my physical A4000, simply because 90% of all the Amiga games use PAL over NTSC.
Which version of Linux are you running?
slaapliedje