FCP X does not have an analogous concept to tracks in a Pro Tools timeline, so a converted project will look different in Pro Tools compared with FCP X. X2Pro uses the names of clip roles to sort the media. In the Pro version of X2Pro you can control which roles are added to the AAF and what their order is.
X2Pro faithfully translates your audio timeline along with L-cuts, J-cuts, volume adjustments, fade handles, markers and transitions (linear cross fades) as well as the incredibly powerful FCP-X compound clips.
X2Pro gives a clear warning when it comes across elements of a sequence which it does not currently translate such as panning, timemaps and effects. Auditions must be finalized first before exporting the XML to X2Pro.
Try loading the FCP XML back into Final Cut Pro X and ensure that the timeline and media is the same as in the original project. If it is not, then FCP has not exported sufficient information for X2Pro to be able to recreate the project in an AAF.