Caps alone on stock Viper shocks lower the spring preload but don't change the stock spring rates, so the OEM damping will still be adequate for the setup (if you were happy with the stock ride). When you lower the ride height w/Eibachs it involves going to a higher spring rate to prevent bottoming, and the stock non-adjustable damping is no longer a match to the springs. Not surprised if it is bouncy.
Spring caps are just like an adjustable spring perch (with only one setting!) which backs off spring preload by a fixed amount and therefore reduces ride height. This is equivalent to backing down the spring perch on a true adjustable coilover (MCS, KW Penske, etc.) by a half-inch or so. At one point Vipair took this a step further and made a product that couples a fully adjustable spring perch to a stock Viper shock. Don't know if Steve still sells these, but the product again runs into the issue of higher-rate aftermarket springs mated to a shock with fixed damping optimized for the factory springs.