If you see more than one color on a bar when setting up your charts for Renko with MQ Trender Pro, you probably missed a step in the setup video. As described in the setup video, when adding MQ Trender Pro to your Renko charts, you want to hide the underlying Renko bars, leaving just the MQ Trender Pro 2.0 indicator to show the bars. This will alleviate the dual colors on the bars.
Here's the link to the video on how to set up Renko charts in TradeStation, which shows how to hide the underlying Renko bars (it's at around the 7-minute point):
In general, you only want to have one indicator coloring the bars on any chart on any platform, so you wouldn't want to use two bar-coloring indicators simultaneously on any chart, such as MQ Trender Pro 2.0 and Value Bars. Unfortunately, you'll need to choose your favorite, and use the other indicator on another chart.