Ah yes, TexturePacker can do some strange things to the orders of tiles. I’m assuming here that you used Gimp to slice your tileset into individual tiles so that TexturePacker could extrude them for you and output a new tileset. Three things to keep in mind are the naming of your tiles, the algorithm setting in TexturePacker, and the max size settings in TexturePacker.
Usually Gimp’s slice command names tiles as slice_0_0, slice_0_1 and so on. This is a format TexturePacker works well with. However if the names are in the format of slice1, slice 2… slice10, you’ll run into a problem. In this case slice10 will often immediately follow slice1. The solution is to pad the numbers with zeroes so that slice1 is slice01, slice2 is slice02, and so forth.
In TexturePacker, under Layout, you want the Algorithm set to Basic and the Sort By set to Name. Further down you should make sure Allow Rotation and Enable Auto Alias are unchecked, and Trim is set to None.
TexturePacker will fill the allotted Max Size from left to right, top to bottom. If fewer tiles will fit across the image than in your source tileset, the row will be truncated, as will the next and the next in a cascading fashion until your tiles appear scrambled. The solution is to alter your Max Size settings until everything fits. Count the number of tiles in one row of your source tileset and then check the number of tiles in one row in TexturePacker. If Fewer tiles fit in a row in TexturePacker than increase the Max Size W: setting until the correct number fits. Do the opposite if too many tiles are present in the row. Eventually everything should snap into place as it should be.