Filter issues

I am new to CCD imaging with filters. Started last night with L filter and I thought everything was going will. L frame was sharp and in focus with no start trails. subs were 360 sec. Im using astro tec 65EQD Sequence generator Pro with auto focus and Moonlite focuser. But when I changes to R and B filter I started getting star trails on the same 360 sec subs. I auto focus before every filter change. Guiding seemed to remain the same. I switched back to L and took another 360 sec sub and there was no star trails. I just noticed there is a delay setting in the filter wheel settings could this be something that could be affecting this issue