Learning of deep neural networks (DNN) using Resistive Processing Unit (RPU) architecture is energy-efficient as it utilizes dedicated neuromorphic hardware and stochastic computation of weight updates for in-memory computing. Charge Trap Flash (CTF) devices can implement RPU-based weight updates in DNNs. However, prior work has shown that the weight updates (V_T) in CTF-based RPU are impacted by the non-ideal program time of CTF. The non-ideal program time is affected by two factors of CTF. Firstly, the effects of the number of input pulses (N) or pulse width (pw), and secondly, the gap between successive update pulses (t_gap) used for the stochastic computation of weight updates. Therefore, the impact of this non-ideal program time must be studied for neural network training simulations. In this study, Firstly, we propose a pulse-train design compensation technique to reduce the total error caused by non-ideal program time of CTF and stochastic variance of a network. Secondly, we simulate RPU-based DNN with non-ideal program time of CTF on MNIST and Fashion-MNIST datasets. We find that for larger N (~1000), learning performance approaches the ideal (software-level) training level and, therefore, is not much impacted by the choice of t_gap used to implement RPU-based weight updates. However, for lower N (<500), learning performance depends on T_gap of the pulses. Finally, we also performed an ablation study to isolate the causal factor of the improved learning performance. We conclude that the lower noise level in the weight updates is the most likely significant factor to improve the learning performance of DNN. Thus, our study attempts to compensate for the error caused by non-ideal program time and standardize the pulse length (N) and pulse gap (t_gap) specifications for CTF-based RPUs for accurate system-level on-chip training.