It's not a problem related to "where" the Arduino software comes, but to the OS itself.
On my Xubuntu 11.04 I used Arduino IDE from Arduino site; after upgrading the system, ArduinoISP stopped working.
On my brand-new laptop, bought 10 days ago, I installed Arch Linux, and the ArduinoISP doesn't work too.
Both of them, curiously, use Kernel 3.0: Xubuntu 11.04 used 2.6.38.
Today I tried a Luigino328 on my Arch system and it showed the same error. Then I tried my UNO on a netbook with Mint Linux with kernel 2.6.38 and... it worked!!!
At work, I have a PC with Ubuntu 10.4 (kernel 2.6.xx) and ArduinoISP works.... so the problem is related to most recent distros with new kernel.
I mean, ArduinoISP isn't compatible with something from that kernel, something different that drives the USB ports, but I don't know what.