Turkish Accelerator and Radiation LAboratory (TARLA) is an accelerator based oscillator mode free electron laser (FEL) facility under construction. The acceleration beam-line includes a fundamental buncher (FB) in order to confine the electron beam into a compressed bunch. In this study, we demonstrate the commissioning tests of 500 W RF amplifier powering FB and present the phase stability dependence of the pressure and temperature of the water cooling line under long time run conditions. As the disturbing effects break down the synchronization between the particle and RF power during acceleration, the reasons disquieting the stability of the RF amplifier are investigated. One reason which disturbs the stability is the variation in the phase of the output power. Phase variation of the output power of the RF amplifier measured as ∼ 10 deg/ • C in average initially, which is beyond permitted variation levels by the controller electronics, namely the Low Level RF system (LLRF), is decreased to less than ∼ 0.45 deg/ • C by incorporating a phase shifter. In addition, this phase variation reduction is accompanied with a reflected power at the output of the RF amplifier decline from 4.3 W (36.33 dBm) down to 3 mW (4.7 dBm) by utilizing a circulator, which is also important and desirable in terms of protection of the electronics in the long term run. As ensuring phase stability in the output power is very important, this work may serve as a guide since the documentation regarding the output power dependence of the water cooling line for long term run is very limited.