Why do my controls stop working when I start a new game?

Solution 1:

Kirby 64: The Crystal Shards is listed in Project 64 as "Issues (Plugin)" because, according to the Game FAQ included with the emulator:

Missing life meter (eggs) on HUD - we have heard from users that after the first boss the meter is displayed normally. Or the problem may come and go at different points in the game. Exact cause is uncertain, very likely something in the core.

Project64 2.0.0.6 beta fixes this issue, but you'll have to be a donor to download the beta. If you don't want to spend $20, then Mupen64 will fix the issue.

As for the controls, Kirby 64 is one of the oddballs that uses the D-Pad instead of the control stick. If you're having trouble with all the other buttons, check out NRage's Input Plugin.