Hey there,
It's hard to know exactly what's going on without seeing it, but if disabling the ARP causes bizarre behavior, there must still be some settings hanging around from an old patch. Make sure you're starting from a fresh program (Go to "Program->Initialize"). In z3ta, the Arpeggiator is (I'd say somewhat confusingly) grouped with the Low Frequency Oscillators. In the top right pane of the interface, far right button should be "AR". Click that and make sure pattern is set to off.
You'll also need to make sure your oscillators are routed to the filter that you're using. In each oscillator there's a slider for "Bus" - make sure it's all the way at the top if you're using filter #1.
If it still sounds funky, it could be because Zeta is defaulting to a low-quality mode to save CPU. Mine defaults to draft-quality, which does cause it to sound pretty gritty. To fix that go to "Options" and make sure both Real-time and Render Quality are set to at least 1.0, or even 2x oversampling.
That ought to do it...