We demonstrate the generation of phase-stable mJ-pulse pairs at programmable inter-pulse delays up to hundreds of nanoseconds. A detailed investigation of potential sources for phase shifts during the parametric amplification of the selected pulses from a Ti:Sapphire frequency comb is presented, both numerically and experimentally. It is shown that within the statistical error of the phase measurement of 10 mrad, there is no dependence of the differential phase shift over the investigated inter-pulse delay range of more than 300 ns. In combination with nonlinear upconversion of the amplified pulses, the presented system will potentially enable short wavelength (<100 nm), multi-transition Ramsey-frequency comb spectroscopy at the kHz-level. © 2013 Optical Society of America.