Yes its a bug during upload caused from the old transfer rate calculation that was disabled (well obviously not fully
Since it is "the old" stuff it has no influence on anything else it just runs into a dead end and should not cause any other problems. Except dumping tons of text into your error log during uploads. But since its happening only every 10 seconds there should be no performance problems from it.
The fix for it is already in CVS.
System crashes are most likely not caused by Phex. Possible problems can come from faulty Java VM implementations, or most likely system driver or bus resource sharing problems.
Phex can put a high load on system devices like network card and disk drives. When I had some troubles with system crashes while using P2P, I found out that my network card, graphic card and disk controller shared the same IRQ and made the systems go crazy. Also removing all unnecessary USB devices can give a lot relieve on system resources.
Each USB device reserves system bus resources, so remove card readers, joysticks and these kind of things if you dont need them. Or if possible switch your USB device (printer, scanner) off.
Hope that helps.