basically pj64 is designed for D3d cards like NVIDIA geforces (jabo made his gfx plugin on a TNT M64) and Radeon cards work well.
u will need jabos D3D 1.3, but also a program called Direct Control where u can disable AGP Texturing (or something like that). theres another post that addresses this more clearly. although despite this, u wil still suffer severe gfx probs unless u update ur card.
Well, I have a v3 too, and PJ64 runs ok on it(not speedy but playable) I use jabo's d3d, sound and input. Maybe your prob is that K6 you have. I though those things have died a long time ago. It has a stinking FPU performance, so it was recomended for business use, not gaming. Uhn, if it can help (after all this i've stated), I'm using the default options for all plugins except the vid. I checked the box "Change blend mode if invalid for video card" under the emulation tab of the video config.