Whenever I run Tixati and download stuff, the entire PC becomes horribly slow.
Firefox takes 16 minutes to open!

The moment I close Tixati, it's back to opening in normal time. It's not only Firefox, it is any operation that mildly requires the HDD.

Also, DL speeds are not going above 3MB/s (I have a 10MB/s connection) when I have more than two DLs running.

Neither x86 or x64 Tixati work well. It is running fine with 400 seeding and 15 downloading (using the full connection speed) on a Intel Atom x86 1.6GHz / 2GB DDR3 Netbook!?

PC is a FX-6300 4.5GHz / 8GB DDR3 1600MHz and is hanging with 5 downloads and 70 seeds.

Any ideas?

All of the sympthons united, this is directly related to the Hard-Disk not capable of handling that many random accesses, so check for fragmentation, or something else bottlenecking permanent data I/O.