as far as I know the jumper has to be set before ever creating a partition
and that it's supposed to be specific to windows XP (though 2k is also affected)
if there's already a partition on the disk, adding the jumper most likely causes the disk's controller to be confused
which might be why the system can't see the disk,
have you attempted to realign the partition with the WDAlign boot CD?
or manually aligning the partition to proper 4K sector boundaries?
that downward spiking is most likely because the drive is having to write accross the sector 4KB boundaries
and because of that it has to wait another revolution before it can see the first sector again
in artificial / simulated 512byte sectors there are 16 sectors simulated on 2 4KB sectors,
the drive reports 512byte sectors at the interface but handles the data on disk as 4KB sectors
this was supposed to be only an XP / 2K etc. problem as those OS demand 512byte sectored HDD's
but it would seem that it's a problem to LInux also and I wouldn't be surprised if Unix & Mac's suffer the same grief
I have 2 of the EARS 1TB HDDs installed in my XP-32 system and after the WDALign tool was used
I get better performance though I still get the initial lag of the translation on first accesses of files / folders
but once the file read or write has started the performance is comparable to any other 512byte sectored HDD
but I wouldn't say that the performance is any better