The reverser in the ES44C4 will get stuck if it is in the forward or reverse position when setting a route in free roam. The CC liveries for freight cars do not show up in the livery menu when spawning cars in free roam. CC Liveries will not show up for multiple if not all freight cars in the following scenarios, Cajon Pass, Sherman Hill, Horseshoe Curve, and The Sand Patch Grade.
Best to put the DLC and issue you are referring to directly into the thread title. ("A Few Issues" is likely to not catch any attention) As for the ES44C4 and other locos, always set your path immediately after taking over the loco, before touching any controls, as sometimes an initialisation script will be triggered on service activation (= setting a path, which turns a static consist into a service). Having already moved some controls can mess with the ini script.